EPA 620/R-05/004
July 2005
Condition of Estuaries of California for 1999:
A Statistical Summary
Office of Research and Development
U.S. Environmental Protection Agency
Washington, DC 20460
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List of Authors
Walter G. Nelson, Henry Lee II, Janet 0. Lamberson
Author Affiliations
Western Ecology Division, National Health and Environmental Effects Research
Laboratory, U.S. Environmental Protection Agency, Newport OR 97365
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Preface
This document is one of a series of statistical summaries for the western states, coastal
component of the nationwide Environmental Monitoring and Assessment Program
(EMAP). The focus of the study during 1999 was the small estuaries of Washington,
Oregon, and California (excluding Puget Sound, the main channel of the Columbia
River, and San Francisco Bay). This document is the first annual statistical summary for
the State of California estuaries (excluding San Francisco Bay). EMAP-West began as
a partnership of the States of California, Oregon and Washington, the National Oceanic
and Atmospheric Administration (NOAA), and the U.S. Environmental Protection
Agency (EPA). The program is administered through the EPA and implemented
through partnerships with a combination of federal and state agencies, universities and
the private sector.
The appropriate citation for this report is:
Nelson, Walter G., Lee II, Henry, Lamberson, Janet 0. 2005. Condition of
Estuaries of California for 1999: A Statistical Summary. Office of Research and
Development, National Health and Environmental Effects Research Laboratory,
EPA 620/R-05/004.
Disclaimer
The information in this document has been funded wholly or in part by the U.S.
Environmental Protection Agency under Cooperative Agreements with the state of
California (CR 827870 ) and an Inter Agency Agreement with the National Marine
Fisheries Service (DW13938780). It has been subjected to review by the National
Health and Environmental Effects Research Laboratory and approved for publication.
Approval does not signify that the contents reflect the views of the agency, nor does
mention of trade names or commercial products constitute endorsement or
recommendation for use.
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Acknowledgments
Western Coastal EMAP involves the cooperation of a significant number of federal,
state, and local agencies. The project has been principally funded by the U.S.
Environmental Protection Agency Office of Research and Development. The following
organizations provided a wide range of field sampling, analytical and interpretive
support in their respective states through individual cooperative agreements with EPA:
Washington Department of Ecology, Oregon Department of Environmental Quality,
Southern California Coastal Water Research Program (SCCWRP). The Northwest
Fisheries Science Center, National Marine Fisheries Service, National Oceanic and
Atmospheric Administration provided field support and analysis offish pathologies
through a cooperative agreement with EPA. Other research organizations provided
additional scientific support through subcontracts with these lead organizations. Moss
Landing Marine Laboratory provided the field crews for collection of samples in
California under contract to SCCWRP.
The U.S. Geological Survey, Columbia Environmental Research Center, through the
Biomonitoring Environmental Status and Trends (BEST) Program, provided analyses for
H4IIE bioassay-derived 2,3,7,8-tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ)
for exposure of fish to planar halogenated hydrocarbons. Through their Marine
Ecotoxicology Research Station, BEST also provided two bioassays on sediment
porewater toxicity, the sea urchin Arbacia punctulata fertilization toxicity and embryo
development toxicity tests.
Project wide information management support was provided by SCCWRP as part of
their cooperative agreement.
Many individuals within EPA made important contributions to Western Coastal EMAP.
Critical guidance and vision in establishing this program was provided by Kevin
Summers of Gulf Ecology Division. Virginia Engle and Linda Harwell of Gulf Ecology
Division were extremely helpful with issues on data analysis. Tony Olsen of Western
Ecology Division has made numerous comments which have helped to improve the
quality of this document. Lorraine Edmond of the Region 10 Office of EPA, and
Terrence Fleming of the Region 9 Office of EPA, have ably served as the regional
liaisons with the state participants in their regions. Robert Ozretich of WED performed a
detailed review of the database contents used for this analysis, and we additionally
thank him for his extensive quality assurance review of this document.
The success of the Western Coastal pilot has depended on the contributions and
dedication of many individuals. Special recognition for their efforts is due the following
participants:
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Washington Department of Ecology
Casey Cliche
Margaret Dutch
Ken Dzinbal
Christina Ricci
Kathy Welch
Oregon Department of Environmental Quality
Mark Bautista
Greg Coffeen
Curtis Cude
Paula D'Alfonso
RaeAnn Haynes
Dan Hickman
Bob McCoy
Greg McMurray
Greg Pettit
Chris Redmond
Crystal Sigmon
Daniel Sigmon
Scott Sloane
Southern California Coastal Water Research Project (SCCWRP)
Larry Cooper
Steve Weisberg
Moss Landing Marine Laboratory
Russell Fairey
Cassandra Roberts
San Francisco Estuary Institute
Bruce Thompson
University of California Davis
Brian Anderson
National Oceanic and Atmospheric Administration
National Marine Fisheries Service, Northwest Fisheries Science Center
Bernie Anulacion
Tracy Collier
Dan Lomax
Mark Myers
Paul Olson
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U.S. Geological Survey
Biomonitoring of Environmental Status and Trends Program (BEST)
Christine Bunck
Columbia Environmental Research Center
Don Tillet
Marine Ecotoxicology Research Station
Scott Carr
Gulf Breeze Project Office
Tom Heitmuller
Steve Robb
Pete Bourgeois
U.S. Environmental Protection Agency
Office of Research and Development
Tony Olsen
Steve Hale
John Macauley
Region 9
Terrence Fleming
Janet Hashimoto
Region 10
Lorraine Edmond
Gretchen Hayslip
Indus Corporation
Patrick Clinton
VI
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Table of Contents
Preface iii
Disclaimer iii
Acknowledgments iv
Table of Contents vii
List of Figures x
List of Tables xvi
Executive Summary xviii
1.0 Introduction 1
1.1 Program background 1
1.2 The California Context for a Coastal Condition Assessment 2
1.3 Objectives 3
2.0 Methods 5
2.1 Sampling Design and Statistical Analysis Methods 5
2.1.1 Background 5
2.1.2 Sampling Design 6
2.1.2.1 1999 California Design 6
2.1.2.2 Overall West Coast Design 8
2.2 Data Analysis 15
2.3 Indicators 18
2.3.1 Water Measurements 21
2.3.1.1 Hydrographic Profile 21
VII
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2.3.1.2 Water Quality Indicators 22
2.3.2 Sediment Toxicity Testing 23
2.3.2.1 Sediment Collection for Toxicity Testing, Chemical
Analysis and Grain Size 23
2.3.2.2 Laboratory Test Methods 23
2.3.2.2.1 Amphipod Toxicity Tests 23
2.3.2.2.2 Sea Urchin Toxicity Tests 25
2.3.3 Biotic Condition Indicators 26
2.3.3.1 Benthic Community Structure 26
2.3.3.2 Fish Trawls 27
2.3.3.3 Fish Community Structure 28
2.3.3.4 Fish Contaminant Sampling 28
2.3.3.5 Fish Contaminant Chemistry Analyses 29
2.3.3.6 Fish Gross Pathology 30
2.3.4 Sediment Chemistry 30
2.4 Quality Assurance/ Quality Control 33
2.4.1 QA of Chemical Analyses 33
2.4.2 QA of Taxonomy 41
2.5 Data management 43
2.6 Unsamplable Area 43
3.0 Indicator Results 45
3.1 Habitat Indicators 45
3.1.1 Water Depth at Sample Sites 45
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3.1.2 Salinity 45
3.1.3 Water Temperature 45
3.1.4 pH 46
3.1.5 Sediment Characteristics 46
3.1.6 Water Quality Parameters 46
3.1.7 Water Column Stratification 49
3.2 Exposure Indicators 68
3.2.1 Dissolved Oxygen 68
3.2.2 Sediment Contaminants 68
3.2.2.1 Sediment Metals 68
3.2.2.2 Sediment Organics 88
3.2.3 Sediment Toxicity 95
3.2.3.1 Amoelisca abdita 95
3.2.3.2 Eohaustorius estuarius 95
3.2.3.3 Arbacia ounctulata 95
3.2.4 Tissue Contaminants 102
3.3 Biotic Condition Indicators 112
3.3.1 Infaunal Species Richness and Diversity 112
3.3.2 Infaunal Abundance and Taxonomic Composition 113
3.3.3 Demersal Species Richness and Abundance 121
4.0 References 124
IX
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List of Figures
Figure 2-1. Location of California EMAP survey sites in Northern California from the
Oregon Border to the Garcia River 10
Figure 2-2. Location of California EMAP survey sites in Northern and Central California
from the Russian River to the Santa Ynez River 11
Figure 2-3. Location of California EMAP survey sites in Central and Southern California
from Santa Barbara to the Mexican border 12
Figure 3.1-1. Percent area (and 95% C.I.) of California small estuaries vs. MLLW
corrected bottom depth 50
Figure 3.1-2. Percent area (and 95% C.I.) of Northern California rivers vs. MLLW
corrected bottom depth 50
Figure 3.1-3. Percent area (and 95% C.I.) of California small estuaries vs. salinity of
bottom waters 51
Figure 3.1-4. Percent area (and 95% C.I.) of Northern California rivers vs. salinity of
bottom waters 51
Figure 3.1-5. Percent area (and 95% C.I.) of California small estuaries vs. temperature
of bottom waters 52
Figure 3.1-6. Percent area (and 95% C.I.) of Northern California rivers vs. temperature
in bottom waters 52
Figure 3.1-7. Percent area (and 95% C.I.) of California small estuaries vs. pH in bottom
waters 53
Figure 3.1-8. Percent area (and 95% C.I.) of Northern California rivers vs. pH in bottom
waters 53
Figure 3.1-9. Percent area (and 95% C.I.) of California small estuaries vs. percent silt-
clay of sediments 54
Figure 3.1-10. Percent area (and 95% C.I.) of Northern California rivers vs. percent silt-
clay of sediments 54
Figure 3.1-11. Percent area (and 95% C.I.) of California small estuaries vs. percent
total organic carbon of sediments 55
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Figure 3.1-12. Percent area (and 95% C.I.) of Northern California rivers vs. percent
total organic carbon of sediments 55
Figure 3.1-13. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean concentration of chlorophyll a 56
Figure 3.1-14. Percent area (and 95% C.I.) of Northern California rivers vs. water
column concentration of chlorophyll a 56
Figure 3.1-15. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean nitrate concentration 57
Figure 3.1-16. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean nitrate concentration 57
Figure 3.1-17. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean nitrite concentration 58
Figure 3.1-18. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean nitrite concentration 58
Figure 3.1-19. Percent area (and 95% C.I.) of California small estuaries vs. water
column ammonium concentration 59
Figure 3.1-20. Percent area (and 95% C.I.) of Northern California rivers vs. water
column ammonium concentration 59
Figure 3.1-21. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean total nitrogen (nitrate + nitrite + ammonium) concentration. . . 60
Figure 3.1-22. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean total nitrogen (nitrate + nitrite + ammonium) concentration. . . 60
Figure 3.1-23. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean orthophosphate concentration 61
Figure 3.1-24. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean orthophosphate concentration 61
Figure 3.1-25. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean ratio of total nitrogen (nitrate + nitrite + ammonium) concentration
to total orthophosphate concentration 62
XI
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Figure 3.1-26. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean ratio of total nitrogen (nitrate + nitrite + ammonium) concentration
to total orthophosphate concentration 62
Figure 3.1-27. Percent area (and 95% C.I.) of California small estuaries vs. water
column total suspended solids concentration 63
Figure 3.1-28. Percent area (and 95% C.I.) of Northern California rivers vs. water
column total suspended solids concentration 63
Figure 3.1-29. Percent area (and 95% C.I.) of California small estuaries vs. percent
light transmission at a reference depth of 1 m 64
Figure 3.1-30. Percent area (and 95% C.I.) of Northern California rivers vs. percent light
transmission at a reference depth of 1 m 64
Figure 3.1-31. Percent area (and 95% C.I.) of California small estuaries vs. water
column Secchi depth 65
Figure 3.1-32. Percent area (and 95% C.I.) of California small estuaries vs. water
column stratification index 66
Figure 3.1-33. Percent area (and 95% C.I.) of Northern California rivers vs. water
column stratification index 66
Figure 3.1-34. Percent area (and 95% C.I.) of California small estuaries vs. Aot
stratification index 67
Figure 3.1-35. Percent area (and 95% C.I.) of Northern California rivers vs. Aot
stratification index 67
Figure 3.2-1. Percent area (and 95% C.I.) of California small estuaries vs. dissolved
oxygen of bottom waters 69
Figure 3.2-2. Percent area (and 95% C.I.) of Northern California rivers vs. dissolved
oxygen of bottom waters 69
Figure 3.2-3. Percent area (and 95% C.I.) of California small estuaries vs. dissolved
oxygen of surface waters 70
Figure 3.2-4. Percent area (and 95% C.I.) of Northern California rivers vs. dissolved
oxygen of surface waters 70
Figure 3.2-5. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of arsenic 77
xii
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Figure 3.2-6. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of arsenic 77
Figure 3.2-7. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of cadmium 78
Figure 3.2-8. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of cadmium 78
Figure 3.2-9. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of chromium 79
Figure 3.2-10. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of chromium 79
Figure 3.2-11. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of copper 80
Figure 3.2-12. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of copper 80
Figure 3.2-13. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of lead 81
Figure 3.2-14. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of lead 81
Figure 3.2-15. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of mercury 82
Figure 3.2-16. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of mercury 82
Figure 3.2-17. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of nickel 83
Figure 3.2-18. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of nickel 83
Figure 3.2-19. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of selenium 84
Figure 3.2-20. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of selenium 84
XIII
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Figure 3.2-21. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of silver 85
Figure 3.2-22. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of silver 85
Figure 3.2-23. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of tin 86
Figure 3.2-24. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of tin 86
Figure 3.2-25. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of zinc 87
Figure 3.2-26. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of zinc 87
Figure 3.2-27. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of total PAH's 92
Figure 3.2-28. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of total PAH's 92
Figure 3.2-29. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of total PCB 93
Figure 3.2-30. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of total PCB 93
Figure 3.2-31. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of total DDT 94
Figure 3.2-32. Percent area (and 95% C.I.) of California small estuaries vs. percent
control corrected survivorship of Ampelisca abdita 97
Figure 3.2-33. Percent area (and 95% C.I.) of Northern California rivers vs. percent
control corrected survivorship of Ampelisca abdita 97
Figure 3.2-34. Percent area (and 95% C.I.) of California small estuaries vs. percent
control corrected survivorship of Eohaustorius estuarius 98
Figure 3.2-35. Percent area (and 95% C.I.) of Northern California rivers vs. percent
control corrected survivorship of Eohaustorius estuarius 98
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Figure 3.2-36. Percent area (and 95% C.I.) of California small estuaries vs. percent
fertilization success of Arbacia punctulata eggs for the 100% water quality
adjusted porewater concentration 99
Figure 3.2-37. Percent area (and 95% C.I.) of California small estuaries vs. percent
fertilization success of Arbacia punctulata eggs for the 50% water quality
adjusted porewater concentration 99
Figure 3.2-38. Percent area (and 95% C.I.) of California small estuaries vs. percent
fertilization success of Arbacia punctulata eggs for the 25% water quality
adjusted porewater concentration 100
Figure 3.2-39. Percent area (and 95% C.I.) of California small estuaries vs. percent
embryonic development success of Arbacia punctulata for the 100% water
quality adjusted porewater concentration 100
Figure 3.2-40. Percent area (and 95% C.I.) of California small estuaries vs. percent
embryonic development success of Arbacia punctulata for the 50% water quality
adjusted porewater concentration 101
Figure 3.2-41. Percent area (and 95% C.I.) of California small estuaries vs. percent
embryonic development success of Arbacia punctulata for the 25% water quality
adjusted porewater concentration 101
Figure 3.3-1. Percent area (and 95% C.I.) of California small estuaries vs. total number
of species of benthic infauna 118
Figure 3.3-2. Percent area (and 95% C.I.) of Northern California rivers vs. total number
of species of benthic infauna 118
Figure 3.3-3. Percent area (and 95% C.I.) of California small estuaries vs. H' diversity
of the benthic infaunal community 119
Figure 3.3-4. Percent area (and 95% C.I.) of Northern California rivers vs. H' diversity
of the benthic infaunal community 119
Figure 3.3-5. Percent area (and 95% C.I.) of California small estuaries vs. total
abundance of benthic infauna 120
Figure 3.3-6. Percent area (and 95% C.I.) of Northern California rivers vs. total
abundance of benthic infauna 120
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List of Tables
Table 2-1. California sampling sites with station coordinates of locations sampled. 13
Table 2-2. Core environmental indicators for the EMAP Western Coastal survey. . 19
Table 2-3. Environmental indicators under development or conducted by
collaborators during the EMAP Western Coastal survey 20
Table 2-4. Compounds analyzed in sediments and fish tissues 31
Table 2-5. Summary of EMAP-Coastal chemistry sample collection,
preservation, and holding time requirements for sediment and fish tissues. . 32
Table 2-6. Units, method detection limits (MDL), reporting limits (RL),
analytical method, and responsible laboratory for sediment chemistry 36
Table 2-7. Units, method detection limits (MDL), reporting limits (RL),
analytical method, and responsible laboratory for tissue chemistry 38
Table 2-8. Summary of performance of California analytical laboratories
with regard to QA/QC criteria for analysis of reference materials,
matrix spike recoveries, and relative percent differences (RPD)
of duplicates 40
Table 2-9. Listing of primary and QA/QC taxonomists by taxon and region for
the 1999 Western Coastal EMAP study 42
Table 3.2-1. Summary statistics for sediment metal concentrations
(ug/g, dry weight) for the California small estuary stations (N=47) 75
Table 3.2-2. Summary statistics for sediment metal concentrations
(ug/g, dry weight) for the Northern California river stations (N=26) 76
Table 3.2-3. Summary statistics for sediment organic pollutants
(ng/g, dry weight) for the California small estuary stations (N=47) 90
Table 3.2-4. Summary statistics for sediment organic pollutants
(ng/g, dry weight) for the Northern California river stations (N=26) 91
Table 3.2-5. The species composition and relative abundance of
the three fish groups used in the tissue residue analysis from
California small estuaries 105
XVI
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Table 3.2-6. The species composition and relative abundance of
the three fish groups used in the tissue residue analysis from
Northern California rivers 105
Table 3.2-7. Fish tissue residues of metals (ug/g wet weight) in
California small estuaries 106
Table 3.2-8. Fish tissue residues of metals (ug/g wet weight) in
Northern California rivers 108
Table 3.2-9. Fish tissue residues of total PCBs, total DDT and additional
pesticides (ng/g wet weight) in California small estuaries 110
Table 3.2-10. Fish tissue residues of total PCBs, total DDT and additional
pesticides (ng/g wet weight) in Northern California rivers 111
Table 3.2-11. Geometric means of tissue lipid content (% wet weight) in
composite samples of three groups offish from California small
estuaries and Northern California rivers 111
Table 3.3-1. Summary of benthic indices for the California small
estuaries (N = 47), and the stations in the Northern California
rivers (N = 25) 115
Table 3.3-2. Abundance, taxonomic grouping, and classification of the
numerically dominant benthic species in the California
small estuaries (N=47) 116
Table 3.3-3. Abundance, taxonomic grouping, and classification of
the numerically dominant benthic species in the Northern
California rivers (N=25) 117
Table 3.3-4. Mean number of fish captured per trawl, mean number of
fish species per trawl, and mean abundance of the ten numerically
dominant fish species in the California small estuaries (N=36) 122
Table 3.3-5. Mean number of fish captured per trawl, mean number of
fish species per trawl, and mean abundance of the ten numerically
dominant fish species in the Northern California rivers (N=2) 123
XVII
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Executive Summary
As a part of the National Coastal Assessment (NCA), the Western Pilot Study under the
Environmental Monitoring and Assessment Program (EMAP) initiated a five year
Coastal component in 1999. The objectives of the program were: to assess the
condition of estuarine resources of Washington, Oregon and California based on a
range of indicators of environmental quality using an integrated survey design; to
establish a baseline for evaluating how the conditions of the estuarine resources of
these states change with time; to develop and validate improved methods for use in
future coastal monitoring and assessment efforts in the western coastal states; and to
transfer the technical approaches and methods for designing, conducting and analyzing
data from probability based environmental assessments to the states and tribes.
For California, the focus of the study during 1999 was the small estuaries of the state,
excluding San Francisco Bay, which was sampled during the second year of the
program in 2000. The study utilized a stratified, random sampling design, with the base
study consisting of 50 sites probabilistically assigned within the small estuaries of
California. Additionally, an intensification study was conducted that consisted of 30
sites distributed among the mouths of river dominated estuaries in northern California.
The two data sets were analyzed separately. Cumulative distribution functions (CDFs)
were produced using appropriate sampling area weightings to represent the areal extent
associated with given values of an indicator variable for both the California small
estuaries base study and the Northern California rivers study.
The environmental condition indicators used in this study included measures of: 1)
general habitat condition (depth, salinity, temperature, pH, total suspended solids,
sediment characteristics), 2) water quality indicators (chlorophyll a, nutrients), 3)
pollutant exposure indicators (dissolved oxygen concentration, sediment contaminants,
fish tissue contaminants, sediment toxicity), and 4) benthic condition indicators (diversity
and abundance of benthic infaunal and demersal species, fish pathological anomalies).
Reflecting the fact that the sampling effort for California small estuaries study spanned
both the Columbian and Californian Biogeographic Provinces, the indicators of general
habitat condition showed wide ranges of values, e.g. bottom water temperatures from
10.1 to 32.1 °C . The Northern California rivers showed a narrower range of bottom
water temperatures from 11.6 °C to 21.9 °C. About 39% of the area of the California
small estuaries had sediments composed of sands, about 46 % was composed of
muddy sands, and about 15 % was composed of muds. The Northern California rivers
had relatively greater proportions of estuarine area characterized by sands (68%), and
less area characterized by muds (4%) or muddy sands (32%). The 90th percentile of
area of both the California small estuaries and the Northern California rivers had a
sediment TOC level of 1.3 %. The pH of bottom water ranged from 6.6 to 10.2, with
values of >9 tending to be associated with low salinity locations.
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There was no geographic pattern to high values of chlorophyll a. All water quality
indicators generally showed similar patterns in their CDFs, with high values being
observed in a very small percentage of estuarine area, thus generating extensive right
hand tails to CDF distributions. For example, the average water column concentration of
nitrate of California small estuaries ranged from 3.4 to 3404 ug L"1, but only 2% of
estuarine area had nitrate values that exceeded concentrations of 300 ug L"1.
Approximately 69% of estuarine area of California small estuaries, and 76% of estuarine
area in Northern California rivers, had molar ratios of average water column total
nitrogen to total phosphorus (N/P) values < 16, suggesting nitrogen limitation.
Approximately 8% of area of California small estuaries and approximately 4% of area of
Northern California rivers had a light transmission of < 10% at 1 m. Approximately 63
% of total estuarine area of California small estuaries showed a Secchi depth > 3 m.
Northern California Rivers were too shallow to measure Secchi depth. There was little
indication of water column stratification within the California small estuaries or Northern
California rivers sampled. The limited stratification is consistent with the large tidal
amplitude across much of the region, which should lead to a high degree of water
column mixing.
Among pollutant exposure indicators, approximately 7% of estuarine area for the
California small estuaries had bottom water dissolved oxygen concentrations < 5 mg/L,
and no values were below 3.75 mg/L. There were no observations in the Northern
California rivers of bottom dissolved oxygen concentration < 5 mg/L.
High values of potentially toxic metals generally occurred in a very small percentage of
the estuarine area sampled, with maximum values of many of the metals being
observed in the highly urbanized Los Angeles Harbor (cadmium, copper, lead, mercury,
selenium, silver, tin, zinc). With the exception of nickel for which the Effects Range
Median concentration (ERM) is unreliable, only chromium exceeded the ERM in >10%
of the area of either the California small estuaries or Northern California Rivers.
Eighteen percent of area of California small estuaries and 61 % of the area of the
Northern California rivers had undetectable concentrations of PAHs. Seventy percent of
area of California small estuaries and 84 % of the area of the Northern California rivers
had non-detectable levels of total PCB's. Highest levels of organic contaminants
generally were associated with urbanized estuaries of southern California. Seventy-four
percent of the area of the California small estuaries had undetectable levels of DDT, as
did all area of the Northern California rivers.
XIX
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Sediment toxicity tests with the amphipod Ampelisca abdita found control corrected
survivorship < 80 % in only about 1 % of area of California small estuaries.
Approximately 39% of the area of the Northern California rivers had control corrected
mean survivorship of A. abdita in sediment bioassays < 80%. Approximately 18.8% of
the area of the California small estuaries had control corrected mean survivorship of
Eohaustorius estuarius in sediment bioassays < 80%. Approximately 24.1% of the area
of the Northern California rivers had control corrected mean survivorship of E. estuarius
in sediment bioassays < 80%.
Sediment pore water bioassays with three treatment levels of serial dilution were
conducted only for the California small estuaries using the sea urchin Arbacia
punctulata. Approximately 21.5 % of the area of the California small estuaries had
control corrected mean percent fertilization of A. punctulata eggs of < 90 % in the 100%
porewater treatment. For the 50 % porewater treatment, 6.7% of estuarine area had
values < 93% fertilization. For the 25 % porewater treatment, 5.8 % of estuarine area
had values < 95% fertilization.
Approximately 95 % of the area of the California small estuaries had control corrected
mean percent embryo development success A. punctulata of < 53 % in the 100%
porewater treatment. For the 50 % porewater treatment, 57.4 % of estuarine area had
values < 96 % embryo development success. For the 25 % porewater treatment, 2.7 %
of estuarine area had values < 93 % embryo development success (Figure 3.2 -41).
Consistently obtaining the target organisms (flatfish) for tissue analysis of contaminants
proved difficult, and tissue analyses were conducted for only 33 stations in the
California small estuaries and 14 stations in the Northern California rivers. Thus
cumulative distribution functions were not computed. There was no consistent spatial
pattern in location of maximum fish tissue metal concentrations. The highest
concentrations of aluminum, chromium and nickel were in samples from the Big River
and the highest concentration of manganese was in the Klamath River, in the Northern
California river samples. The highest concentrations of zinc and silver were in Big
Lagoon, the highest selenium and lead values were in Long Beach Harbor, and the
highest copper value occurred in San Diego Bay. The highest arsenic value was in
Humboldt Bay.
Maximum fish tissue residues for total PCBs and pesticides were associated with
urbanized estuaries in California, which were also associated with highest sediment
concentrations of these contaminants. Tissue residues of DDT and its metabolites were
considerably higher than other pesticides measured.
xx
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Benthic infaunal community samples were obtained using either grabs or combining
smaller corers to obtain equivalent surface area at 47 sites in the California small
estuaries and 25 sites in the Northern California rivers. Reflecting the wide geographic
distribution of sampling, a total of 552 non-colonial benthic taxa were recorded. Species
richness ranged from 1 to 95 taxa per sample in the California small estuaries, while the
maximum species richness in the Northern California rivers was 35 taxa. Lowest
species richness tended to be associated with low salinity sites, and highest species
richness was associated with salinities > 30 psu. About 50% of the area of California
small estuaries had species richness < 33.2 species per sample. The northern
California rivers tended to have lower species richness and H' diversity values, with
50% of the area of these systems having fewer than 6.3 species.
Benthic infaunal abundance averaged 1033 individuals per sample in the California
small estuaries, and 5606 individuals per sample in the Northern California rivers.
About 50% of the area of California small estuaries had mean infaunal abundance <
368 individuals per sample. In the Northern California estuaries rivers, 50% of the area
had benthic densities < 2864 individuals per sample. The California small estuary
stations tended to be dominated by annelids while the Northern California rivers were
dominated by crustaceans. Two amphipod species (Americorophium spinicorne, A.
salmonis) had extremely high abundances in several Northern California rivers. The
most abundant species in the California small estuary stations was nonindigenous, and
nonindigenous or cryptogenic (suspected nonindigenous) species comprised 6 of the 13
numerically dominant species. In comparison, only one of the 10 numerically dominant
species in Northern California rivers was nonindigenous while one other was
cryptogenic.
The 1999 Western Coastal EMAP study provides the first probabilistic assessment of
the condition of the small estuaries of California. When these data are combined with
the data collected in 2000 from the San Francisco Bay estuarine system, there will exist
the first comprehensive data set for evaluating the overall condition of all estuarine
systems of California.
XXI
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1.0 Introduction
1.1 Program background
Safeguarding the natural environment is fundamental to the mission of the US
Environmental Protection Agency (EPA). The legislative mandate to undertake this part
of the Agency's mission is embodied, in part, in the Clean Water Act (CWA). Sections of
this Act require the states to report the condition of their aquatic resources and list those
not meeting their designated use (Section 305b and 303d respectively). Calls for
improvements in environmental monitoring date back to the late 1970's, and have been
recently reiterated by the U. S. General Accounting Office (U.S. GAO, 2000). The GAO
report shows that problems with monitoring of aquatic resources continue to limit states'
abilities to carry out several key management and regulatory activities on water quality.
At the national level, there is a clear need for coordinated monitoring of the nation's
ecological resources. As a response to these needs at state and national levels, the
EPA Office of Research and Development (ORD) has undertaken research to support
the Agency's Regional Offices and the states in their efforts to meet the CWA reporting
requirements. The Environmental Monitoring and Assessment Program (EMAP) is one
of the key components of that research and EMAP-West is the newest regional
research effort in EMAP. From 1999 through 2005, EMAP-West has worked to develop
and demonstrate the tools needed to measure ecological condition of the aquatic
resources in the 14 western states in EPA's Regions 8,9, and 10.
The Coastal Component of EMAP-West began as a partnership with the states of
California, Oregon and Washington, the National Oceanic and Atmospheric
Administration, and the Biomonitoring of Environmental Status and Trends Program
(BEST) of the U.S. Geological Survey to measure the condition of the estuaries of
these three states. Sampling began during the summer of 1999 and the initial phase of
estuarine sampling was completed in 2000. Data from this program is the basis for
individual reports of condition for each state, as well as to providing data to the National
Coastal Assessment.
The US EPA's National Coastal Assessment (NCA) is a five-year effort led by EPA's
Office of Research and Development to evaluate the assessment methods it has
developed to advance the science of ecosystem condition monitoring. This program will
survey the condition of the Nation's coastal resources (estuaries and offshore waters)
by creating an integrated, comprehensive coastal monitoring program among the
coastal states to assess coastal ecological condition. The NCA is accomplished
through strategic partnerships with all 24 U.S. coastal states. Using a compatible,
probabilistic design and a common set of survey indicators, each state conducts the
survey and assesses the condition of their coastal resources independently. Because
of the compatible design, these estimates can be aggregated to assess conditions at
the EPA Regional, biogeographical, and national levels.
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This report provides a statistical summary of the data from the first year of sampling
(1999) for the estuarine systems of the state of California, exclusive of the San
Francisco Bay estuary.
1.2 The California Context for a Coastal Condition Assessment
Nationwide, growth of the human population is disproportionally concentrated in the
coastal zone (Culliton et al., 1990). Within the California coastal region, greatest
population expansion has been in the major urban areas of the San Francisco Bay area,
and much of Southern California. These metro areas are either directly located on
coastal water bodies, or like Sacramento, are on major rivers and thus influence the
estuaries downstream. While development around the estuaries to the north of Point
Reyes in California has been less intense, substantial population growth is taking place
across the region. Human population growth in the coastal zone of the west is a
principal driver for many ecological stressors such as habitat loss, pollution, and nutrient
enhancement which alter coastal ecosystems and affect the sustainability of coastal
ecological resources (Copping and Bryant, 1993). Increased globalization of the
economy is a major driver influencing the introduction of exotic species into port and
harbors. Major environmental policy decisions at local, state and federal levels related
to land use planning, growth management, habitat restoration and resource utilization
will determine the future trajectory for estuarine conditions of the western United States.
Changes associated with human population growth in the western coastal region tend to
be most obvious in the larger, urban areas, but all coastal resources have been
subjected to significant alterations over the last 150 years. In one of the earliest
ecological alterations, sea otters, a known ecological keystone species (Simenstad et
al, 1978), were largely removed from western coastal ecosystems by 1810, and
populations have never recovered. The wave of western mining in the late 1800's had
limited effects on most coastal systems in terms of altering estuaries or causing
chemical pollution (Burning, 1996). Outside of the major ports, western estuaries are
believed to have generally low concentrations of toxic pollutants because of relatively
low population densities and low levels of heavy industry (Copping and Bryant, 1993),
but data for most estuaries are sparse.
Resource exploitation for agriculture, logging and damming each resulted in major
changes to land use practices throughout the California coastal region. Sedimentation
problems associated with land use changes may be especially acute along the west
coast north of San Francisco because of the combination of steep coastal watersheds,
high rainfall, and timber harvesting. Nutrient and sediment loadings from population
centers will augment the increased flux of these materials resulting from the larger scale
watershed alterations associated with logging of the coastal mountains (Howarth et al.,
1991). For example it is known that around Chesapeake Bay, deforestation associated
with human settlement and agricultural clearing led to a 100% increase in sediment
accumulation rates (Cooper and Brush, 1991) during the 1800's.
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The increase in regional and international marine commerce along the west coast has
resulted in the introduction of nonindigenous species. The effect of nonindigenous
species on estuarine habitats has only recently come under scrutiny (Carlton and
Geller, 1993; Lee et al., 2003), but the potential for ecological transformation is great.
Multiple studies have shown that San Francisco Bay has been extensively invaded by
nonindigenous species, and that invaders are now among the dominants in a number of
habitats (Cohen and Carlton, 1998). It is not presently known whether the smaller
estuaries of California are similarly invaded.
Within estuaries, benthic environments are areas where many types of impacts from the
stressors described above will tend to accumulate. Deposition of toxic materials,
accumulation of sediment organics, and oxygen deficiency of bottom waters typically
have a greater impact on benthic organisms than on planktonic and nektonic organisms
because of their more sedentary nature. Long-term studies of the macrobenthos
(Reish, 1986, Holland and Shaughnessey, 1986) demonstrate that macrobenthos is a
sensitive indicator of pollutant effects. Benthic assemblages are also closely linked to
both lower and higher trophic levels, as well as to processes influencing water and
sediment quality, and therefore appear to integrate responses of the entire estuarine
system (Leppakoski, 1979; Holland and Shaughnessey, 1986).
Biologically, the California component of the EMAP Western Coastal study area is
represented by two biogeographic provinces, the Columbian Province which extends
from the Washington border with Canada to Point Conception, California, and the
Californian Province which extends from Point Conception to the Mexican border.
Within the two California biogeographic provinces, there are also major distinctions in
the distribution of the human population. Major population centers surround San
Francisco Bay and most of the estuaries of southern California. In contrast, the region
of coastline from north of San Francisco Bay to the Oregon border has a much lower
population density. While it may be presumed that the magnitude of anthropogenic
impacts will tend to show a similar distribution, this hypothesis has not yet been tested
for West Coast estuaries.
1.3 Objectives
The EMAP sampling program conducted in California in 1999 was a first year
component of the larger EMAP Western Coastal Program, which has the following
objectives:
1. To assess the condition of estuarine resources of Washington, Oregon and California
based on a range of indicators of environmental quality using an integrated survey
design;
2. To establish a baseline for evaluating how the conditions of the estuarine resources
of these states change with time;
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3. To develop and validate improved methods for use in future coastal monitoring and
assessment efforts in the western coastal states;
4. To transfer the technical approaches and methods for designing, conducting and
analyzing data from probability based environmental assessments to the states and
tribes.
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2.0 Methods
2.1 Sampling Design and Statistical Analysis Methods
2.1.1 Background
The EMAP approach to evaluating the condition of ecological resources is described in
reports such as Diaz-Ramos et al. (1996), Stevens (1997), Stevens and Olsen (1999)
and is also presented in summaries provided on the internet at the URL:
http://www.epa.gov/nheerl/arm/index.htm
A brief summary from these documents follows.
Given the fact that it is generally impossible to completely census an extensive
resource, such as the set of all estuaries on the west coast, a more practical approach
to evaluating resource condition is to sample selected portions of the resource using
probability based sampling. Studies based on random samples of the resource rather
than on a complete census are termed sample surveys. Sample surveys offer the
advantages of being affordable, and of allowing extrapolations to be made of the overall
condition of the resource based on the random samples collected. Survey
methodologies are widely used in national programs such as forest inventories,
agricultural statistics survey, national resource inventory, consumer price index, labor
surveys, and such activities as voter opinion surveys.
A survey design provides the approach to selecting samples in such a way that they
provide valid estimates for the entire resource of interest. Designing and executing a
sample survey involves five steps: (1) creating a list of all units of the target population
from which to select the sample, (2) selecting a random sample of units from this list, (3)
collecting data from the selected units, (4) summarizing the data with statistical analysis
procedures appropriate for the survey design, and (5) communicating the results. The
list or map that identifies every unit within the population of interest is termed the
sampling frame.
The sampling frame for the EMAP Western Coastal Program was developed from
USGS 1:100,000 scale digital line graphs and stored as a CIS data layer in ARC/INFO
program. A series of programs and scrips (Bourgeois et al., 1998) was written to
create a random sampling generator (RSG) that runs in ArcView. Site selection
consisted of using the RSG to first overlay a user-defined sampling grid of hexagons
over the spatial resource which consisted of all estuaries of the west coast, including
California. The area of the hexagons was controlled by adjusting the distance to
hexagon centers, and by defining how many sample stations were to be generated for
each sampling region. After the sampling grid was overlaid on the estuarine resource,
the program randomly selected hexagons and randomly located a sampling point within
the hexagon. Only one sampling site was selected from any hexagon selected. The
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program determined whether or not a sampling point fell in water or on land, and sites
that fell on land were not included. The RSG is run iteratively until a hexagon size is
determined which generates the desired number of sampling sites within the resource
(Bourgeois etal., 1998).
Hexagon size may be different for classes of estuarine systems of different areal extent.
The final data analysis which provides the estimates of resource condition then weights
the samples based on the area of the estuarine class. Stevens (1997) terms this a
random tessellation stratified (RTS) survey design applied to each estuarine resource
class.
2.1.2 Sampling Design
2.1.2.1 1999 California Design
The assessment of condition of small estuaries conducted in 1999 was the first phase of
a planned two year comprehensive assessment of all estuaries of the state of California.
The complete assessment requires the integrated analysis of data collected from the
small estuarine systems in 1999 and the large estuarine system (San Francisco Bay) in
2000. The intent of the design is to be able to combine data from all stations for
analysis, using the inclusion probabilities, defined as the total estuarine area in km2
within a given design stratum (= estuarine size class), to weight the representation of
samples in the combined analysis. The two year California sampling program was a
component of the overall two year Western Coastal EMAP sampling program designed
to characterize the condition of the estuarine resources of Washington, Oregon and
California (2.1.2.2. below).
The California sampling frame was constructed as a CIS coverage that would include
the total area of the estuarine resource of interest. Available CIS coverages were not
perfect representations of the estuarine resource, and so the coverages were defined to
ensure that they included the resource, but may have possibly included some nearby
land or inland water. The inland boundary of the sampling frame was defined as the
head of salt water influence, while the seaward boundary was defined by the confluence
with the ocean. Sample locations could fall within any water depth contained within the
estuarine resource which was bounded by the shoreline. In some cases, extremely
shallow sites were deemed inaccessible by field crews with the sampling gear specified
(Section 2.6). Emergent salt marsh areas were not included in the sampling frame.
The 1999 California base sampling design (termed the "California small estuaries" study
in this report) included all estuaries of the state with the exception of San Francisco
Bay, and consisted of a total of 50 sites (Sites 1-50, Table 2-1). Approximately equal
sampling effort was placed in each of three estuarine size classes (<5, 5-25 and >25
km2) to ensure some level of sampling across the entire range of estuarine sizes.
Sample selection utilized three hexagonal grid sizes reflecting these three estuary size
classes: 0.86; 7.79; and 12.50 km2. No alternate or oversample sites were selected
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during the design, and thus any sites which could not be sampled were not replaced.
Improvements to subsequent versions of the RSG produced after this study allow
incorporation of alternate sample sites.
The estuarine systems on the northern California coast, with the exception of the Arcata
and Humboldt Bay systems, are relatively poorly studied. A number of the rivers which
discharge directly into the Pacific Ocean have been listed as failing to meet designated
uses and have been designated for development of Total Maximum Daily Load (TMDL)
limits. At the request of the Region 9 Office of EPA, an intensification study was
conducted to sample the river mouth estuaries of both listed and non-listed systems of
Northern California (Figure 1). The purpose of this assessment was to generate
baseline information on these resources and to determine if there were any differences
in the estimates of condition for the two categories of estuarine resource.
Sites (n=30) were randomly selected at the mouths of the river systems in Northern
California (Sites 51-80, Table 2-1). The 1999 Northern California estuarine river mouth
sampling study is termed the "Northern California rivers" study in this report to
distinguish it from the base study. The design for this intensification study incorporated
6 differing hexagonal grid sizes: 0.0346; 0.0498; 0.0585; 0.0800; 0.0914; and 0.1060
km2. The hexagonal grid sizes were used to locate random sample sites within a total
of seven strata representing differing total areas of the estuarine resource in these
Northern California river mouth systems (see Table 2.1 for association of grid size with
estuary stratum). Sample sites were divided equally between streams with and without
TMDL listings (Table 2-1). No alternate or oversample sites were selected during the
design, and thus any sites which could not be sampled were not replaced.
While the intent of the California design was to be able to combine all study sites
seamlessly into combined analyses, an inadvertent design change occurred which
somewhat complicates interpretation of results. In defining the target population for the
Northern California sites, a restriction of sampling to a distance of 0.25 km from the
estuarine mouth was imposed. This definition differs from that of the remainder of the
west coast assessment which used a target population defined by the head of salt in the
estuary. In order to prevent duplicative sampling effort, the northern California small
river systems had been excluded from the frame for the base California study. Thus, a
small area (approximately 10 km2) above 0.25 km and below head of tide was
inadvertently omitted from the California sampling frame.
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2.1.2.2 Overall West Coast Design
For the sake of completeness, the entire West Coast design will be described. For the
state of Washington, the1999 design included only small estuaries along the coastline
outside of the Puget Sound system, and consisted of a total of 50 sites. Tributary
estuaries of the Columbia River located within Washington state were included in the
1999 sampling effort, while the main channel area was not sampled until 2000 (as part
of the 2000 Oregon design). The sampling frame utilized three hexagonal grid sizes to
cover the size range of estuaries: 0.86; 7.79; 36.58 km2. The hexagonal grid sizes were
used to locate random sample sites within a total of four strata representing differing
total areas of the estuarine resource in Washington. To insure some level of sampling
across the entire range of estuarine sizes, sampling effort was partitioned as 10
stations within the smallest estuarine size class, 25 stations within the two strata
representing the medium sized estuaries, and 15 stations in the largest size class. No
alternate or oversample sites were included in the design.
The Oregon 1999 design included only small estuaries of the state and consisted of 50
sites. Tributary estuaries of the Columbia River located within Oregon were included in
the 1999 sampling effort, while the main channel area was not sampled until 2000. The
sampling frame for small estuaries utilized four hex sizes to cover the size range of
estuaries: 1.24; 3.46; 4.58; and 7.28 km2. Approximately equal sampling effort was
placed in each of the four estuarine strata, which represented differing size classes of
estuaries, to insure some level of sampling across the entire range of estuarine sizes.
An intensive sampling effort was designed for Tillamook Bay, where a total of 30 sites
were selected using a hex size of 1.04 km2. No points from the base design were
placed in Tillamook Bay. All sites were combined for analysis. No alternate or
oversample sites were included in the design.
The Washington 2000 sampling design included only the large "estuary" of Puget
Sound and its tributaries. Site selection for this estuary used a combined approach in
order to allow collaboration with a survey previously conducted by NOAA under the
NOAA National Status and Trends Program. The overall design combined the existing
NOAA probability based, randomized monitoring design with the EMAP Western
Coastal study design. The EMAP hexagonal grid was extended to include Canadian
waters at the north end of Puget Sound, and then was overlaid on the existing NOAA
monitoring sites. If a NOAA site fell within a hexagon, the site was designated as the
EMAP sampling point. If not, a random site was selected based on the EMAP
protocols. The design incorporated three different hex sizes, two covering most of the
Puget Sound region (86.6, 250.28 km2), and one used for intensifying in the region of
the San Juan Islands (21.65 km2). There were 41 stations selected based on the NOAA
sampling stations, in addition to 30 new EMAP stations, of which 10 were associated
with the San Juan Islands. No alternate or oversampling sites were included in the
design frame.
8
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The Oregon 2000 design included only the main channel area of Columbia River. The
Columbia River system was split into two subpopulations, the lower, saline portion and
the upper freshwater portion, with hex sizes of 13.85 and 5.4 km2 and total numbers of
stations of 20 and 30, respectively. No alternate or oversample sites were included in
the design.
The 2000 California design included only San Francisco Bay and its tributaries. Site
selection for this estuary used a combined approach in order to allow collaboration with
a survey being conducted by NOAA under the NOAA National Status and Trends
Program. An EMAP sampling design was developed specifically for NOAA to implement
a multiyear monitoring program to characterize condition of the small systems within the
San Francisco Bay. To insure complete coverage of the bay for the EMAP Western
Coastal study, the NOAA design was augmented with a sampling design which split the
Bay into two subpopulations (open bay and smaller surrounding systems). For the open
bay, a hex size of 36.58 km2 was used and 31 sites were generated. For the smaller
systems, a different hexagon size (3.46 km2) was used to generate 19 sites for
sampling. This grid was overlaid on the newly designed NOAA small systems
monitoring project. If a NOAA site fell within a hexagon, the site was used as the
sampling point. If not, a random point was generated based on the standard
randomization routines used by Western Coastal EMAP as part of the National Coastal
Assessment. No alternate or oversample sites were selected.
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k
SMITH RIVER (CA)
-h-
WILSON CREEK •
KLAMATH RIVER \
BIG LAGOON f®
LITTLE RIVER "~?J
ARCATABAYjjp
HUMBOLDT BAY Jf
EEL RIVERA'
BEAR RIVER P
NOYO RIVER
CASPAR CREEK
BIG RIVER
ALBION RIVER *
ELK CREEK
GARCIA RIVER
-124°
OREGON
CALIFORNIA
-122°
50
Intensive Study Sites
0 50
Base Study Sites
100
ISO
200 km
Figure 2-1. Location of California EMAP survey sites in Northern California from the
Oregon Border to the Garcia River.
10
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X
RUSSIAN RIVERA
lESTERO AMlfflC AND
ISTEROSAN^
TOMALES /"to V'^-4 7~2
BAY j|^ ^ 1^y=^"-qr
DRAKESBAY
SANTA CRUZ HARBOR V
PAJARORTVER
MONTEREY HARBOR /••&
CARMELBAY *"
CALIFORNIA
MORRO BAY p
SAN LUIS OBISPO BAY
SANTA YNEZRTVER
• Intensive Study Sites $ Base Study Sites
100 0 100 200km
Figure 2- 2. Location of California EMAP survey sites in Northern and Central California
from the Russian River to the Santa Ynez River.
11
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CALIFORNIA
SANTA BARBARA ®
HA88011 VENTURA RIVER »
CHANNEL ISLANDS HARBOR®
,
POINT MUGCr \
LAGOON \
KING HARBOR* ^_^OS ANGELES MVER
LOS ANGELES HARBOR
LONG BEACH HARBOR
\
DANA POINT ®x
~\ HARBOR %x
SANTA MARGARITA RIVER *
AGUA HEDIONDA CREEK
SAN DIEGO RTVER j
SAN DIEGO BAY
-119° -777c
9 Base Study Sites
100 0 100 200 km
Figure 2-3. Location of California EMAP survey sites in Central and Southern California
from Santa Barbara to the Mexican border.
12
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Table 2-1. California sampling sites with station coordinates of locations sampled. The
northern California river TMDL study sites are noted as either Y = TMDL Site, N = Non-
TMDL site. Frame area represents the total estuarine area within a stratum.
EMAP Sta. No. Latitude Longitude Estuary
CA99-0001
CA99-0002
CA99-0003
CA99-0004
CA99-0005
CA99-0006
CA99-0007
CA99-0008
CA99-0009
CA99-0010
CA99-001 1
CA99-0012
CA99-0013
CA99-001 4
CA99-0015
CA99-001 6
CA99-001 7
CA99-0018
CA99-0019
CA99-0020
CA99-0021
CA99-0022
CA99-0023
CA99-0024
CA99-0025
CA99-0026
CA99-0027
CA99-0028
CA99-0029
CA99-0030
CA99-0031
CA99-0032
CA99-0033
CA99-0034
CA99-0035
CA99-0036
CA99-0037
CA99-0038
CA99-0039
CA99-0040
CA99-0041
CA99-0042
CA99-0043
CA99-0044
CA99-0045
CA99-0046
CA99-0047
CA99-0048
CA99-0049
CA99-0050
CA99-0051
CA99-0052
CA99-0053
CA99-0054
CA99-0055
CA99-0056
CA99-0057
CA99-0058
CA99-0059
CA99-0060
41.162
40.837
40.824
40.720
40.703
38.287
38.263
38.249
38.104
38.015
38.006
38.006
38.002
36.961
36.859
36.633
36.628
36.537
36.525
35.346
35.318
35.171
35.173
35.161
34.692
34.407
34.354
34.180
34.167
34.097
33.844
33.777
33.742
33.755
33.741
33.730
33.743
33.724
33.719
33.461
33.234
33.145
33.143
32.772
32.755
32.759
32.727
32.726
32.651
32.639
41 .945
41 .947
41 .944
41.941
41.937
41 .606
41 .605
41 .547
41 .546
41 .541
-124.118
-124.117
-124.142
-124.238
-124.258
-123.028
-123.012
-122.978
-122.848
-122.917
-122.910
-122.873
-122.865
-122.019
-121.801
-121.845
-121.853
-121.930
-121.936
-120.847
-120.858
-120.737
-120.725
-120.710
-120.597
-119.693
-119.309
-119.230
-119.227
-119.079
-118.395
-118.242
-118.252
-118.154
-118.177
-118.256
-118.140
-118.214
-118.233
-117.702
-117.412
-117.342
-117.339
-117.210
-117.248
-117.219
-117.215
-117.180
-117.129
-117.138
-124.201
-124.204
-124.197
-124.196
-124.196
-124.100
-124.101
-124.081
-124.075
-124.079
Big Lagoon
Arcata Bay
Arcata Bay
Humboldt Bay
Humboldt Bay
Bodega Bay
Bodega Bay
Bodega Bay
Tomales Bay
Drakes Bay
Drakes Bay
Drakes Bay
Drakes Bay
Santa Cruz Harbor
Pajaro River
Monterey Harbor
Monterey Harbor
Carmel Bay
Carmel Bay
Morro Bay
Morro Bay
San Luis Obispo Bay
San Luis Obispo Bay
San Luis Obispo Bay
Santa Ynez River
Santa Barbara Harbor
Ventura River
Channel Islands Harbor
Channel Islands Harbor
Point Mugu Lagoon
King Harbor
Los Angeles River
Los Angeles Harbor
Long Beach Harbor
Long Beach Harbor
Los Angeles Harbor
Long Beach Harbor
Los Angeles Harbor
Los Angeles Harbor
Dana Point Harbor
Santa Margarita River
Agua Hedionda Creek
Agua Hedionda Creek
Mission Bay
San Diego River
San Diego River
San Diego Bay
San Diego Bay
San Diego Bay
San Diego Bay
Smith River (Ca)
Smith River (Ca)
Smith River (Ca)
Smith River (Ca)
Smith River (Ca)
Wilson Creek
Wilson Creek
Klamath River
Klamath River
Klamath River
Hex Size Frame Area
km2
7.79
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
12.5
7.79
0.86
7.79
7.79
7.79
7.79
7.79
7.79
7.79
7.79
7.79
0.86
0.86
0.86
0.86
0.86
0.86
0.86
0.86
12.5
7.79
7.79
12.5
7.79
12.5
12.5
0.86
0.86
0.86
0.86
7.79
0.86
0.86
12.5
12.5
12.5
12.5
0.10
0.106
0.106
0.106
0.106
0.08
0.08
0.0346
0.0346
0.0346
km2
102.651
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
268.504
102.651
13.837
102.651
102.651
102.651
102.651
102.651
102.651
102.651
102.651
102.651
13.837
13.837
13.837
13.837
13.837
13.837
13.837
13.837
268.504
102.651
102.651
268.504
102.651
268.504
268.504
13.837
13.837
13.837
13.837
102.651
13.837
13.837
268.504
268.504
268.504
268.504
0.654
0.654
0.654
0.654
0.654
0.014
0.014
0.309
0.309
0.309
Stratum
CA99-002
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-001
CA99-002
CA99-003
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-002
CA99-003
CA99-003
CA99-003
CA99-003
CA99-003
CA99-003
CA99-003
CA99-003
CA99-001
CA99-002
CA99-002
CA99-001
CA99-002
CA99-001
CA99-001
CA99-003
CA99-003
CA99-003
CA99-003
CA99-002
CA99-003
CA99-003
CA99-001
CA99-001
CA99-001
CA99-001
CA99-006
CA99-006
CA99-006
CA99-006
CA99-006
CA99-004
CA99-004
CA99-009
CA99-009
CA99-009
TM[
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N
N
N
N
N
N
N
Y
Y
Y
13
-------
CA99-0061
CA99-0062
CA99-0063
CA99-0064
CA99-0065
CA99-0066
CA99-0067
CA99-0068
CA99-0069
CA99-0070
CA99-0071
CA99-0072
CA99-0073
CA99-0074
CA99-0075
CA99-0076
CA99-0077
CA99-0078
CA99-0079
CA99-0080
41 .028
41 .027
40.644
40.646
40.475
39.427
39.417
39.418
39.361
39.303
39.226
39.225
39.227
39.103
39.102
38.954
38.451
38.449
38.307
38.270
-124.112
-124.109
-124.305
-124.304
-124.388
-123.808
-123.812
-123.809
-123.815
-123.794
-123.770
-123.768
-123.764
-123.707
-123.705
-123.730
-123.127
-123.125
-122.995
-122.976
Little River
Little River
Eel River
Eel River
Bear River
Noyo River
Hare Creek
Hare Creek
Caspar Creek
Big River
Albion River
Albion River
Albion River
Elk Creek
Elk Creek
Garcia River
Russian River
Russian River
Estero Americano
Estero San Antonio
0.08
0.08
0.0914
0.0914
0.08
0.0585
0.08
0.08
0.08
0.0585
0.0914
0.0914
0.0914
0.08
0.08
0.0585
0.0498
0.0498
0.0585
0.0585
0.018
0.018
0.219
0.219
0.018
0.427
0.018
0.018
0.014
0.427
0.219
0.219
0.219
0.014
0.014
0.427
0.104
0.104
0.427
0.427
CA99-005
CA99-005
CA99-01 0
CA99-01 0
CA99-005
CA99-007
CA99-005
CA99-005
CA99-004
CA99-007
CA99-01 0
CA99-01 0
CA99-01 0
CA99-004
CA99-004
CA99-007
CA99-008
CA99-008
CA99-007
CA99-007
N
N
Y
Y
N
Y
N
N
N
Y
Y
Y
Y
N
N
Y
Y
Y
Y
Y
14
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2.2 Data Analysis
Analysis of indicator data was conducted by calculation of cumulative distribution
functions (CDFs), an analysis approach that has been used extensively in other EMAP
coastal studies (Summers et al. 1993, Strobel et al. 1994, Hyland et al. 1996). The
CDFs describe the full distribution of indicator values in relation to their areal extent
across the sampling region of interest. The approximate 95% confidence intervals for
the CDFs also were computed based on estimates of variance. A detailed discussion of
methods for calculation of the CDF's used in EMAP analyses is provided in Diaz-Ramos
etal. (1996).
The Horvitz-Thompson ratio estimate of the CDF is given by the formula:
F(x*) = estimated CDF (proportion) for indicator value x*
n = number of samples
y/= the sample response for site i
x* = the k th CDF response indicator
\ {\y><**
l(y,
-------
The Horvitz-Thompson unbiased estimate of the variance for the ratio estimate is given
by the formula:
"df_+""dd fj_j -\_]
V (F(xk)] = -^ "'" A*'*' X'J •
A/2
N = ^]—, cf,. = /(y < x*) - F(Xk), dj = l(yj < x«) - F(x*)
F(x*) = estimated CDF (proportion) for indicator value x*
f 1 V, < XK
l(y,
-------
When estimating the CDF across several strata, the above estimates for each stratum
must be combined. The equations are
F(xk) = estimated CDF
A
Fjfa) = estimated CDF for stratum i
A, = area for stratum i
S = number of strata
A = total area of all strata
and the variance estimate across strata is
V = estimated variance for all strata
A
Vj = estimated variance for stratum i
A, = area for stratum i
S = number of strata
A = total area of all strata
17
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2.3 Indicators
The condition of California estuarine resources was evaluated by collecting data for a
standard set of core environmental parameters at all stations within the survey (Table 2-
2). Field procedures followed methods outlined in the USEPA National Coastal
Assessment Field Operations Manual (USEPA, 2001 b). The environmental indicators
were similar to those used in previous EMAP estuarine surveys in other regions of the
country (Weisberg et al., 1992; Macauley et al., 1994, 1995; Strobel et al., 1994, 1995;
Hyland et al., 1996, 1998). Indicators were divided into those representing general
habitat condition (Habitat Indicators), condition of benthic and demersal faunal
resources (Biotic Condition Indicators), and exposure to pollutants (Exposure
Indicators). Habitat indicators describe the general physical and chemical conditions at
the study site, and are often important in providing information used to interpret the
results of biotic condition indicators (e.g., salinity and sediment grain size with regard to
benthic community composition). Biotic condition indicators are measures of the status
of the benthic biological resources in response to site environmental conditions. The
Exposure indicators used in this survey quantify the amounts and types of pollutant
materials (metals, hydrocarbons, pesticides) that may be harmful to the biological
resources present. Some indicators may overlap the above categories. For example,
dissolved oxygen is clearly an indicator of habitat condition, but may also be considered
an exposure indicator because of the potentially harmful effects of low dissolved oxygen
levels to many members of the benthic community.
In addition to the core set of indicators, a number of supplemental indicators were
conducted either by EMAP or by external collaborators during the EMAP Western
Coastal survey (Table 2-3). An additional sediment toxicity test was conducted for the
base California stations using the amphipod Eohaustorius estuarius acute toxicity test in
order to compare the sensitivity of this species with Ampelisca abdita, which is the most
commonly used amphipod bioassay species in the EMAP program. Scientists with the
USGS/BEST program conducted two sediment porewater toxicity tests using the sea
urchin Arbacia punctulata (fertilization toxicity test, embryo development toxicity test)
(USGS, 2000), and conducted the H4IIE bioassay (bioassay-derived 2,3,7,8-
tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ)) for exposure offish to planar
halogenated hydrocarbons (USGS, 2001). Results of the sea urchin bioassay tests are
included in the present report, while the details of the H4lle bioassay are provided in
USGS (2001).
18
-------
Table 2-2. Core environmental indicators for the EMAP Western Coastal survey.
Habitat Indicators
Salinity
Water depth
pH
Water temperature
Total suspended solids (TSS)
Chlorophyll a concentration
Nutrient concentrations (nitrate,
nitrite, ammonium, &
orthophosphate)
Percent light transmission
Secchi depth
Percent silt-clay of sediments
Percent total organic carbon (TOC)
in sediments
Benthic Condition Indicators
Infaunal species composition
Infaunal abundance
Infaunal species richness and diversity
Demersal fish species composition
Demersal fish abundance
Demersal fish species richness and
diversity
External pathological anomalies in fish
Exposure Indicators
Dissolved oxygen concentration (DO)
Sediment contaminants
Fish tissue contaminants
Sediment toxicity (Ampelisca abdita
acute toxicity test)
19
-------
Table 2-3. Environmental indicators under development or conducted by collaborators
during the EMAP Western Coastal survey.
Benthic Condition Indicators
West Coast benthic infaunal index - EMAP
Exposure Indicators
Sediment toxicity (amphipod Eohaustorius estuarius acute toxicity test) - EMAP
(California only)
Sediment porewater toxicity (sea urchin Arbacia punctulata fertilization toxicity test)
USGS/BEST1
Sediment porewater toxicity (sea urchin Arbacia punctulata embryo development
toxicity test) - USGS/BEST1
H4IIE Bioassay-derived 2,3,7,8-tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ)
for exposure offish to planar halogenated hydrocarbons - USGS/BEST2
1 USGS, 2000
2 USGS, 2001
20
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2.3.1 Water Measurements
2.3.1.1 Hydrographic Profile
Water column profiles were performed at each site to measure dissolved oxygen (DO),
salinity, temperature, pH, and depth. Both Secchi depth and a measurement of light
attenuation using Photosynthetically Active Radiation (PAR) were made at each station
where possible due to water depth. Methods and procedures used for hydrographic
profiling follow guidance provided in the NCA Quality Assurance Project Plan document
(US EPA, 2001).
Basic water quality parameters were measured by using a hand-held multiparameter
water quality probe Hydrolab Datasonde 4a with a cable connection to a deck display.
Prior to conducting a CTD (Conductivity, Temperature, Depth) cast, the instrument was
allowed 2-3 minutes of warmup while being maintained near the surface, after which,
the instrument was slowly lowered at the rate of approximately 1 meter per second
during the down cast. Individual measurements were made at discrete intervals (with
sufficient time for equilibration) as follows:
Shallow sites (< 2 m) - every 0.5 m interval;
Typical depths (2-10 m) - 0.5 m (near-surface) and every 1-m interval to near-
bottom (0.5 m off-bottom);
Deep sites (>10 m) - 0.5 m (near-surface) and every 1-m interval to 10 m, then at
5-m intervals, thereafter, to near-bottom (0.5 m off-bottom).
Near-bottom conditions were measured at 0.5 m above the bottom by first ascertaining
whether the instrument was on the bottom (slack line/cable), and then pulling it up
approximately 0.5 m. A delay of 2-3 minutes was used to allow disturbed conditions to
settle before taking the near-bottom measurements. The profile was repeated on the
ascent and recorded for validation purposes, but only data from the down trip were
reported in the final data.
Measurements of light penetration were recorded using a hand held LiCor LI-1400 light
meter for conditions at discrete depth intervals in a manner similar to that for profiling
water quality parameters with the hand-held water quality probes. The underwater
(UW) sensor was hand lowered according to the regime described above and at each
discrete interval, the deck reading and UW reading were recorded. If the light
measurements became negative before reaching bottom, the measurement was
terminated at that depth. The profile was repeated on the ascent. As an indicator of
water column light conditions, the transmissivity at 1 m depth was calculated.
The California field crew measured ambient light data in two ways. The Hydrolab
datasonde unit had a LiCor spherical irradiance sensor (LI -193SA) mounted to the
sensor package. For boat deployments, the deck sensor recording ambient light was a
cosine collector (LI-190SA)). However, many of the California sample locations were
21
-------
too shallow to allow sampling from a boat, and required walking in to the sample site. At
these stations, the field crew took ambient irradiance with the spherical sensor in air,
and then took several subsurface readings with the same sensor. The difference in
geometry between the deck reference sensor and submerged sensor was corrected for
during the analysis of light transmission. An empirical comparison of similar LiCor
spherical and flat sensors, both calibrated for air measurements, was conducted. The
spherical sensor collected an average of two times the light measured by the flat
sensor. All ambient light measurements for California stations sampled by boat were
first corrected by this factor. The minimum depth where the first submerged light
reading was taken varied widely among stations, which made inter-station comparison
difficult. Therefore, the submerged and corresponding in air light measurements,
together with the depth of the measurement, were used to compute the light extinction
coefficient k, using the relationship k = (In(l0) - ln(ld))/d , where I0 = in air measure of
light, ld = submerged light, and d = the depth of the first submerged light measurement.
The value of k that was computed was assumed to characterize the light attenuation
down to a depth of 1 m, and light at a depth of 1 m (I1m) was then calculated as I1m = e("
kd), where d = 1m. Percent light transmission at 1m was then computed as (I1m/10) * 100.
Secchi depth was determined by using a standard 20-cm diameter black and white
Secchi disc. The disc was lowered to the depth at which it could no longer be discerned,
then was slowly retrieved until it just reappeared. The depth of reappearance was
recorded as Secchi depth (rounded to the nearest 0.5 m).
2.3.1.2 Water Quality Indicators
The water column was sampled at each site for dissolved nutrients (N and P species),
chlorophyll a concentration, and total suspended solids (TSS) using a Wildco 1.2-liter
stainless steel Kemmerer sampler. At shallow sites (<2 m), water samples were taken at
0.5 m (near-surface) and 0.5 m off-bottom. If the depth was so shallow that the near-
surface and near-bottom overlapped, then only a mid-depth sample was taken. For
sites deeper than 2m, samples were taken at 0.5 m (near-surface), mid-depth, and 0.5
m off-bottom.
For TSS analysis, 1 liter of unfiltered seawater was collected at the depths described
above. The samples were held in 1-L polypropylene bottles on wet ice in the field and
stored at 4°C until analyzed. A second water sample was collected from each of the
same depths and an approximately 1-liter subsample was poured into a clean, wide-
mouth polycarbonate container for the chlorophyll and nutrient analyses. Two
disposable, graduated 50-cc polypropylene syringes fitted with a stainless steel or
polypropylene filtering assembly were used to filter the water sample through 0.7 urn
GFF filters, and the volume of water (up to 200 ml for each syringe) filtered was
recorded. Both filters were carefully removed using tweezers, folded once upon the
pigment side, placed in a prelabeled, disposable petri dish, and capped. The petri dish
was wrapped in aluminum foil, placed in a small styrofoam ice chest with several
pounds of dry ice, and kept frozen until analyzed. The syringe and filtering assembly
22
-------
were washed with deionized water and stored in a clean compartment between
sampling stations. For nutrients, approximately 40 ml of filtrate from the chlorophyll
filtration (surface water) were collected into two prelabeled, clean 60-ml Nalgene
screw-capped bottles, stored in the dry ice chest, and kept frozen on dry ice until
analyzed. Dissolved oxygen was measured with a Hydrolab DO sensor on the Hydrolab
datasonde.
2.3.2 Sediment Toxicity Testing
2.3.2.1 Sediment Collection for Toxicity Testing, Chemical Analysis and Grain
Size
Combined sediment for toxicity testing and chemical analysis was collected at all sites
from the top 2-3 centimeters of surficial sediment. Where possible, sediment grabs
were taken with a 0.1 m2 van Veen sampler. The top 2-3 centimeters of surficial
sediment were scooped from each individual grab, composited in a pre-cleaned
container and homogenized within the container by thorough stirring. Sediment from 1-
9 grabs was composited to collect approximately 6 liters of sediment. Where station
depth precluded sampling with a boat and van Veen grab, the sampling crew walked in
to the sample site, and the top 2-3 cm of sediment at the site was scooped from the
sediment surface and processed similarly to sediment collected by grab. This occurred
at the following: (33 sites in California: CA99-0001, CA99-0015, CA99-0021, CA99-
0025, CA99-0030, CA99-0037, CA99-0041, CA99-0045-46, CA99-0051-57, CA99-
0059-65, CA99-0067-71, CA99-0073-74, CA99-0076, CA99-0079-80). The composited
sediment was held on ice and distributed to individual containers for toxicity testing and
chemical analyses either on board the research vessel or at the laboratory. Aliquots of
the homogenized sediment were distributed to pre-cleaned containers for analysis of
sediment organics, trace metals, grain size and toxicity testing. Toxicity test sediment
was held at 4°C to await initiation of toxicity testing within 7 days of collection (holding
times for other sample measurements are given in Table 2-5).
2.3.2.2 Laboratory Test Methods
2.3.2.2.1 Amphipod Toxicity Tests
The 10-day, solid-phase toxicity test with the marine amphipod Ampelisca abdita was
used to evaluate potential toxicity of sediments from all sites. Procedures followed the
general guidelines provided in ASTM Protocol E1367-92 (ASTM 1991), the EPA
amphipod sediment toxicity testing manual (USEPA, 1994a), and the EMAP Laboratory
Methods Manual (USEPA 1994b). The Ampelisca test is a 10-d acute toxicity test which
measures the effect of sediment exposure on amphipod survival under static aerated
conditions.
23
-------
Approximately 3-3.5 L of surface sediments (composite of upper 2-3 cm from multiple
grabs) were collected from the sampling sites and stored in glass or polyethylene jars at
4 °C in the dark until testing. Toxicity tests were conducted with subsamples of the same
sediment on which the analysis of organic and trace metal contaminants and other
sediment characteristics was performed.
Ampelisca abdita were collected from San Pablo Bay in the San Francisco Estuary by
Brezina and Associates. Amphipods were shipped via overnight carrier to the Marine
Pollution Studies Laboratory at Granite Canyon, CA, or the Southern California Coastal
Water Research Project (SCCWRP - CA sediments), where the Ampelisca tests were
conducted. Amphipods were acclimated for 2-9 days prior to testing. During the
acclimation period, the amphipods were not fed. Healthy subadult amphipods of
approximately the same size (0.5-1.0 mm Ampelisca] 2-3 mm Eohaustorius) were used to
initiate tests. The general health of each batch of amphipods was evaluated in a reference
toxicity test (i.e., "positive control"), which was run for 96 h in a dilution series with
seawater (no sediment phase) and the reference toxicants cadmium chloride or sodium
dodecyl sulfate (SDS). LC50 values were computed for comparison with other reported
toxicity ranges for the same reference toxicant and test species. Eohaustorius estuarius
were collected from Beaver Creek on the central Oregon coast by Northwest Aquatic
Sciences. This species was shipped and acclimated as described above for A. abdita,
prior to test initiation. Cadmium chloride reference tests were conducted with each batch
of E. estuarius.
Treatments for the definitive tests with field samples consisted of five replicates of each
sediment sample (100% sediment) and a negative control. Control sediment was home
sediment from the amphipod collection sites in San Pablo Bay or Beaver Creek for A.
abdita or E. estuarius, respectively. A negative control was run with each batch of field
samples, which ranged from 4-18 samples per batch. Twenty amphipods were randomly
distributed to each of five replicates per each treatment including the control. Amphipods
were not fed during the tests. All tests were conducted under static conditions with
aeration, and were monitored for water quality (temperature, salinity, dissolved oxygen,
pH, and total ammonia in the overlying water). Target test temperature for A. abdita was
20 °C and target salinity was 28 %o. Test temperature for E. estuarius was 15 °C, and
salinity was 20 %o.
The negative controls provided a basis of comparison for determining statistical differences
in survival in the field sediments. In addition, control survival provided a measure of the
acceptability of final test results. Test results with A. abdita were considered valid if mean
control survival (among the 5 replicates) was ^ 90% and survival in no single control
replicate was less than 80%. Mean control survival for A. abdita was 94% and ranged from
89 - 98% throughout the various tests. Test batches where QA requirements were not met
were not included in the CDF analysis. Test results with E. estuarius were considered valid
if mean control survival (among the 5 replicates) was 90% and survival in any single control
chamber was 85%. Mean control survival for E. estuarius was 97% and ranged from 91-
100% throughout the various tests, and all tests with this species were accepted as valid.
24
-------
One-liter glass containers with covers were used as test chambers. Each chamber was
filled with 200 ml of sediment and 600-800 ml of filtered seawater. The sediment was
press-sieved, through either a 1.0-mm screen for control samples or a 2.0-mm screen for
field samples, to remove ambient fauna prior to placing the sediment in a test chamber.
Light was held constant during the 10-day test to inhibit amphipod emergence from the
sediment, thus maximizing exposure to the test sediment. Air was supplied using oil-free
pumps and glass pipettes inserted into the test chambers. Water tables with recirculating
chiller pumps were used to maintain constant temperatures (20 ± 1 °C for A. abdita, 15 ± 1
°C for E. estuarius). Daily recordings were made of temperature and the number of dead
vs. living animals. On two separate days, near the beginning and end of the 10-day
exposure, two of the five replicate chambers for each treatment were selected randomly
and measured for salinity, dissolved oxygen, pH, and total ammonia in the overlying water.
At the conclusion of a test, the sediment from each chamber was sieved through a 0.5-mm
screen to remove amphipods. The number of animals dead, alive, or missing was recorded.
Sediments with >10% missing animals were re-examined under a dissecting microscope to
ensure that no living specimens had been missed. Amphipods still unaccounted for were
considered to have died and decomposed in the sediment.
A variety of quality control procedures were incorporated to assure acceptability of
amphipod test results and comparability of the data with other studies. As described above,
these provisions included the use of standard ASTM and EMAP protocols, positive controls
run with a reference toxicant, negative "performance" controls run with reference sediment
from the amphipod collection site, and routine monitoring of water quality variables to
identify any departures from optimum tolerance ranges.
2.3.2.2.2 Sea Urchin Toxicity Tests
The Biomonitoring and Environmental Status and Trends Program (BEST) of the U.S.
Geological Survey obtained sediment samples collected by EMAP and conducted two
types of sea urchin toxicity tests. The fertilization and embryological development toxicity
tests were conducted with sediment porewater using gametes of the sea urchin Arbacia
punctulata. Methods and results are described in a technical report (USGS, 2000).
Briefly, sediments for testing were held on ice or refrigerated at 4°C and shipped in
insulated coolers within 7 days to the BEST laboratory. Pore water was extracted from the
test sediments within 24 hours of receipt using a pneumatic device, centrifuged to remove
suspended particulate material, then stored frozen. Sediments that were received by the
BEST laboratory at temperatures exceeding acceptable temperature criteria were
excluded from the CDF analysis.
25
-------
Sediment pore water was thawed two days prior to testing and stored at 4°C. Water
quality parameters (salinity, temperature, DO) were measured in the thawed pore water
and adjusted if necessary. Samples were tested at temperature and salinity of 20 + 2°C
and 30 + 1 ppt. Other water quality parameters that were measured included dissolved
oxygen, pH, sulfide, ammonia and dissolved organic carbon.
Toxicity was determined using percent fertilization and embryological development
(percent normal pluteus stage) as endpoints with gametes of the sea urchin Arbacia
punctulata. Porewater samples were tested over a dilution series at 100, 50 and 25 % of
the water quality adjusted (WQA) porewater sample. Filtered seawater and
reconstituted brine were used as dilution blanks. Reference pore water from an
uncontaminated site in Redfish Bay, TX was included in each test as a negative control.
A dilution series with sodium dodecyl sulfate was used as a positive control. USGS
(2000) assessed toxicity with statistical comparisons among treatments using ANOVA
and Dunnett's one-tailed t-test on the arcsine square root transformed data.
Thirteen test sediment samples arrived at the testing laboratory at temperatures that
exceeded the acceptable temperature criterion. Since it is not known what effect the
elevated temperatures may have on porewater toxicity, test results from these
sediments were excluded from the CDF analysis, leaving a total of 34 stations in the
analysis. Samples excluded were CA99-0014-17, 20-23, 25-26 and 29-30. USGS
(2000) includes toxicity estimations from all samples.
2.3.3 Biotic Condition Indicators
2.3.3.1 Benthic Community Structure
Sediment samples to enumerate the benthic infauna were collected at all sampling sites
unless rocky bottom or other factors prohibited obtaining a benthic sample (see section
2.6). The standard sampling gear was a 0.1 m2 van Veen grab sampler. In California,
sites with a water depth less than approximately 1 meter were sampled with hand-held
cores. At these shallower areas, a composite of sixteen 0.0065 m2 cores were taken,
for a total surface area of 0.1 m2. Eight of the base California stations and 23 of the
Northern California intensive sites were sampled with these cores. To evaluate the
efficiency of smaller sample sizes, a single 0.0065 m2 core was taken from the van
Veen grabs in 24 sites in Southern California. For this analysis, the results from the
sub-cores and the remainder of the van Veen grab were combined.
The majority of the grab and core samples penetrated a minimum of 5 cm deep. The
eleven samples that penetrated 3-4 cm are included in the present analysis. After
collection, samples were sieved through nested 0.5 mm and 1.0 mm mesh screens. An
elutriation process was used to minimize damage to soft-bodied animals and the
material retained on the screens was relaxed in 1 kg of MgS04 per 20 L of seawater for
30 minutes. The residue was then preserved in the field in sodium borate-buffered 10%
formalin.
26
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The preserved samples were sent to the benthic ecology laboratory at the Washington
Department of Ecology where they were transferred to 70% ethanol within 2 weeks of
field collection. The 1.0 mm mesh screen samples were then sorted from the debris.
The 0.5 mm mesh samples were not included as part of EMAP West and were not
sorted. The organisms were then identified to the lowest practical taxonomic level
(most often species), and counted by the primary taxonomists (see Table 2-9).
Secondary QA taxonomists ensured that uniform nomenclature was used across the
entire Western Coastal EMAP region; these recognized taxonomic experts identified
and resolved taxonomic discrepancies among the sets of primary taxonomists. In the
analyses for this report, all insect taxa were grouped as Insecta. Individual insect taxa
will be identified in later versions of the database.
The benthic infaunal data were used to compute total numbers of individuals and total
number of species per 0.1 m2 sample. The Shannon-Weaver information diversity index
H' was calculated (log base 2) per 0.1 m2 sample. Species were classified as native,
nonindigenous, cryptogenic, or indeterminate. Cryptogenic species are suspected
nonindigenous species (Carlton, 1996) while indeterminate taxa are those taxa not
identified to a sufficiently low level to classify as native, nonindigenous, or cryptogenic
(Lee et al.,2003). Species were classified using Cohen and Carlton (1995) as the
primary source and a report by TN and Associates (2001) for taxa not classified by
Cohen and Carlton. The TN and A report specifically classified the benthic species
collected by the 1999 EMAP survey as native, nonindigenous, or cryptogenic.
2.3.3.2 Fish Trawls
Fish trawls were conducted at each site, where possible, to collect fish/shellfish for
community structure and abundance estimates, collect target species for contaminant
analyses, and collect specimens for histopathological examination. In some cases, it
was necessary to use beach seines instead of trawls to collect fish for tissue analysis.
Only trawls were used to evaluate fish community structure because consistency
between beach seines was impossible to maintain. A total of 41 of the 50 base stations
were sampled by trawl, with the remaining 9 stations (CAOO-0001, CAOO-0015, CAOO-
0021, CAOO-0025, CAOO-0027, CAOO-0030, CAOO-0041, CAOO-0045, CAOO-0046)
sampled by seine. Only 2 stations (CAOO-0077, CAOO-0078) of the 30 stations in the
northern California rivers could be sampled by trawl.
Trawls were conducted by using a 16-ft otter trawl with 1.5" mesh in the body and wings
and 1.25 inch mesh in the cod end. Community structure data (i.e, the fish data on
richness and abundance and individual lengths) were based on a trawl(s) of
approximately 10 minute duration. In open water, the trawl was conducted in a straight
line with the site location near center. Timing of the trawl began after the length of
towline had been payed out and the net began its plow. The speed over bottom was
approximately 2 knots. When possible, trawling was conducted for the entire 10-minute
period, after which the boat was placed in neutral and the trawl net retrieved and
brought aboard. In constrained areas where 10 minute trawls were not possible, two 5
27
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minute trawls were conducted. Contents of the bag were emptied into an appropriately
sized trough or livebox to await sorting, identifying, measuring, and sub-sampling.
Trawling was the last field activity performed because of possible disturbance to
conditions at the site. Every effort was made to return any rare or endangered species
back to the water before they suffered undue stress.
A 100' beach seine with 1/8" mesh was used for fish collections in shallow waters.
2.3.3.3 Fish Community Structure
Fish from a successful trawl (full time on bottom with no hangs or other interruptions)
were first sorted by type and identified to genus and species. Up to thirty individuals per
species were measured by using a fish measuring board to the nearest centimeter (fork
length when tail forked, otherwise overall length - snout to tip of caudal). The lengths
were recorded on a field form and a total count made for each species. All fish not
retained for histopathology or chemistry were returned to the estuary.
2.3.3.4 Fish Contaminant Sampling
Several species of demersal soles, flounders, and dabs were designated as target
species for the analyses of chemical contaminants in whole-body tissue. These flatfish
are common along the entire U.S. Pacific Coast and are intimately associated with the
sediments. Where the target flatfish species were not collected in sufficient numbers,
perchiform species were collected. These species live in the water column but feed
primarily or opportunistically on the benthos. In cases where neither flatfish species nor
perchiform species were collected, other species that feed primarily or opportunistically
on the benthos were collected for tissue analysis. The 14 species collected and
analyzed for tissue contaminants were (species occurring in only one or two stations are
identified):
Pleuronectiformes
Citharichthys sordidus - Pacific sanddab
Citharichthys stigmaeus - speckled sanddab
Paralichthys californicus - California halibut
Platichthys stellatus - starry flounder
Pleuronectes vetulus - English sole
Symphurus atricauda - California tonguefish (1 small estuaries station)
Perciformes
Cymatogaster aggregata - shiner perch
Gasterosteus aculeatus - threespine stickleback (1 small estuaries and
1 Northern CA rivers station)
Genyonemus lineatus - white croaker
Paralabrax maculatofasciatus - spotted sand bass (1 small estuaries station)
Paralabrax nebulifer - barred sand bass
28
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Other
Atherinops affinis - topsmelt (1 small estuaries station)
Leptocottus armatus - Pacific staghorn sculpin
Oligocottus rimensis - saddleback sculpin (2 Northern CA rivers stations)
Residues of a suite of metals, PCBs, and pesticides were measured in the whole bodies
offish at 33 stations in the California small estuaries and 14 stations in the Northern
California rivers. The remaining stations were not sampled due to shallow water,
unavailability of fish or other difficulties. At sites where target species were captured in
sufficient numbers, 3 to 30 individuals of a species were combined into a composited
sample. Due to their small size, up to 220 individual Gasterosteus aculeatus
(threespine stickleback) were composited to obtain a sufficient tissue sample at one of
the Northern CA rivers sites. At some sites, fish from more than one species were
sampled and analyzed separately by species. In all cases, the fish were first measured
and recorded on the sampling form as chemistry fish. The fish were then rinsed with site
water, individually wrapped with heavy duty aluminum foil (the length of each individual
fish was imprinted on the foil wrap to facilitate the possible later selection of specific
individuals at the laboratory), and placed together in a plastic, Ziploc™ bag labeled with
the Station ID Code and a Species ID Code (e.g., the first four letters of both the genus
and species). The fish chemistry samples were held on wet ice in the field until they
were transferred to shore and frozen to await laboratory analysis.
2.3.3.5 Fish Contaminant Chemistry Analyses
Neutral organic and metal contaminants were measured in the whole-body tissues of
the fourteen species of fish listed above (Section 2.3.3.4). Contaminant concentrations
were determined for each of the composited tissue samples. A total of 12 inorganic
metals, 21 polychlorinated biphenyls (PCBs,), DDT and its primary metabolites, and an
additional 13 pesticides were measured in the fish samples. PAHs were not measured
in fish tissues because of their rapid metabolism in vertebrates. The analytes measured
in fish and sediments are summarized in Table 2-4. Table 2-5 summarizes the sample
collection, preservation, and holding time requirements for tissue samples. Table 2-6
summarizes the analytical methods used for both sediments and tissues. For tissue
chemistry analyses, the NCA Quality Assurance Program Plan (EPA 2001 a)
recommends that internal standards known as surrogates be run, and suggests that
reported concentrations for analytes be adjusted to correct for recovery of surrogates.
The state analytical laboratories generally used surrogates only as an indication of
whether a re-extraction of a sample was required.
2.3.3.6 Fish Gross Pathology
Any fish pathologies (e.g. tumors) observed on fish collected in the trawls were
photographed, then excised and placed into labeled pathology containers, and put
immediately into Dietrich's solution. Excised tissue included the entire pathology and
some adjacent healthy tissue. Pathology information including container number, fish
29
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species, size, station ID, trawl number, pathology location, description, and sample
depth were recorded onto a Cumulative Fish Pathology Log. At the end of the field
collection, all samples were sent to Dr. Mark Meyers at NMFS/NOAA in Seattle for
analysis. A separate fish pathology report will be prepared by NOAA.
2.3.4 Sediment Chemistry
A total of 15 metals, 21 PCB congeners (PCBs), DDT and its primary metabolites, 12
pesticides, 21 polynuclear aromatic hydrocarbons (PAHs), and total organic carbon
(TOC) were measured in sediments (Table 2-4). With a few additions, this suite of
compounds is the same as measured in the NOAA NS&T Program.
Sediment for chemical analysis was collected from the top 2-3 centimeters in benthic
grabs and stored in pre-cleaned glass containers (see Table 2-5). Sediment samples
for chemical analysis were taken from the same sediment composite used for the
sediment toxicity tests. Approximately 250-300 ml of sediment was collected from each
station for analysis of the organic pollutants and another 250-300 ml for analysis of the
metals and TOC (Table 2-6). Tables 2-6 list the analytical methods used for each
compound. For sediment chemistry analyses, the NCA Quality Assurance Program
Plan (EPA 2001 a) recommended that internal standards known as surrogates be run,
and suggested that reported concentrations for analytes be adjusted to correct for
recovery of surrogates. The state analytical laboratories generally used surrogates only
as an indication of whether re-extraction of a sample was required.
30
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Table 2-4. Compounds analyzed in sediments and fish tissues. PAHs and TOC were analyzed only in sediments.
Toxaphene was analyzed only in tissues.
Polyaromatic Hydrocarbons
(PAHs)
Low Molecular Weight PAHs (sediments only)
1 -methy Inaphthalene
1 -methy Iphenanthrene
2-methy Inaphthalene
2,6-dimethylnaphthalene
2 , 3 , 5 - trimethy Inaphthalene
Acenaphthene
Acenaphthylene
Anthracene
Biphenyl
Fluorene
Naphthalene
High Molecular Weight PAHs (sediments only)
Benz(a)anthracene
Benzo(a)pyrene
Benzo(b)fluoranthene
Benzo(k)fluoranthene
Benzo(g,h,i)perylene
Chrysene
Dibenz(a,h)anthracene
Fluoranthene
Indeno( 1 ,2,3-c,d)pyrene
Pyrene
PCB Congeners
(Congener Number and
Compound)
8: 2,4'-dichlorobiphenyl
18: 2,2',5-trichlorobiphenyl
28: 2,4,4'-trichlorobiphenyl
44: 2,2',3,5'-tetrachlorobiphenyl
52: 2,2',5,5'-tetrachlorobiphenyl
66: 2,3',4,4'-tetrachlorobiphenyl
77: 3,3',4,4'-tetrachlorobiphenyl
1 01 : 2,2',4,5,5'-pentachlorobiphenyl
105: 2,3,3',4,4'-pentachlorobiphenyl
110: 2,3,3',4',6-pentachlorobiphenyl
118: 2,3',4,4',5-pentachlorobiphenyl
126: 3,3',4,4',5-pentachlorobiphenyl
128: 2,2',3,3',4,4'-hexachlorobiphenyl
138: 2,2',3,4,4',5'-hexachlorobiphenyl
153: 2,2',4,4',5,5'-hexachlorobiphenyl
1 70: 2,2',3,3',4,4',5-heptachlorobiphenyl
1 80: 2,2',3,4,4',5,5'-heptachlorobiphenyl
187: 2,2',3,4',5,5',6-heptachlorobiphenyl
195: 2,2',3,3',4,4',5,6-octachlorobiphenyl
206: 2,2',3,3',4,41,5,51,6-nonachlorobiphenyl
209: 2,2'3,3',4,41,5,51,6,6 '-decachlorobiphenyl
DDT and Other
Chlorinated
Pesticides
DDTs
2,4-DDD
4,4'-DDD
2,4'-DDE
4,4'-DDE
2,4'-DDT
4,4'-DDT
Cyclopentadienes
Aldrin
Dieldrin
Endrin
Chlordanes
Alpha-Chlordane
Heptachlor
Heptachlor Epoxide
Trans-Nonachlor
Others
Endosulfan I
Endosulfan II
Endosulfan Sulfate
Lindane (gamma-BHC)
Mirex
Toxaphene (tissue only)
Metals and Misc.
Metals
Aluminum
Antimony (sediment only)
Arsenic
Cadmium
Chromium
Copper
Iron (sediment only)
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Tin (sediment only)
Zinc
Miscellaneous
Total organic carbon
(sediment only)
-------
Table 2-5. Summary of EMAP-Coastal chemistry sample collection, preservation, and holding time requirements for
sediment and fish tissues. Modified from Table 5-3 of the Quality Assurance Project Plan for Coastal 2000 (U.S. EPA,
2000).
Parameter
Container
Volume
Sample Size
Sample
Preservation
Max.
Sampling
Holding Time
Max. Extract
Holding Time
Sediment -
Organics
Sediment -
Metals
Sediment -
3 TOG
Fish tissue
500-ml pre- 250 -300 ml
cleaned glass
125-mlHDPE 100 -150 ml
wide-mouth
bottle
Glass jar 100 -150 ml
Whole fish NA
individually
wrapped in Al
foil, then
placed in
water-tight
plastic bag.
300 g
(approx.)
75- 100 g
(approx.)
30 - 50 ml
(approx.)
NA
Freeze (-18° 1 year
C)
Freeze (-18° 1 year
C)
Cool (4° C) 6 months
Freeze (-18° 1 year
C)
40 days
a
a
40 days
a - No EPA criterion exists. Every effort should be made to analyze the sample as soon as possible following extraction,
or in the case of metals, digestion.
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2.4 Quality Assurance/ Quality Control
The quality assurance/quality control (QA/QC) program for the Western Coastal EMAP
program is defined by the "Environmental Monitoring and Assessment Program
(EMAP): National Coastal Assessment Quality Assurance Project Plan 2001-2004" (US
EPA, 2001 a). The NCA has established Data Quality Objectives (DQO) for estimates of
current status for indicators of condition which are stated as: "For each indicator of
condition, estimate the portion of the resource in degraded condition within ±10% for the
overall system and ±10% for subregions (i.e., states) with 90% confidence based on a
completed sampling regime." An assessment of this standard for the combined
1999/2000 data from the states of Washington, Oregon and California is presented in
the Quality Assurance Appendix of the National Coastal Condition Report II (EPA,
2004). The level of uncertainty for the combined west coast data set for all major
indicators was < 5%.
In general, the quality assurance elements for the EMAP Western Coastal program
included initial training workshops on all sampling and analysis requirements and initial
laboratory capability exercises, program-wide audits of field and laboratory operations,
documentation of chain-of-custody, and maintaining open lines of communication and
information exchange. Information management needs were demonstrated to all
participants by the Western Coastal EMAP information manager. Other quality control
measures were incorporated to assure data reliability and comparability and are
described in the NCA plan. These include the use of standard NCA protocols, routine
instrument calibrations, measures of analytical accuracy and precision (e.g., analysis of
standard reference materials, spiked samples, and field and laboratory replicates),
measures of the quality of test organisms and overall data acceptability in sediment
bioassays (e.g., use of positive and negative controls), range checks on the various
types of data, cross-checks between original data sheets (field or lab) and the various
computer-entered data sets, and participation in intercalibration exercises.
Accuracy is used to estimate systematic error (measured vs. true or expected), while
precision is used to determine random error (variability between individual
measurements). Collectively, they provide an estimate of the total error or uncertainty
associated with an individual measured value. Measurement quality objectives (MQO)
for all NCA field and laboratory parameters are expressed in terms of accuracy,
precision, and completeness goals in the NCA QA Project Plan (US EPA, 2001 a, Table
A7-1). These MQOs were established from considerations of instrument manufacturers
specifications, scientific experience, and/or historical data. However, accuracy and
precision goals may not be definable for all parameters due to the nature of the
measurement type (e.g., fish pathology, no expected value).
2.4.1 QA of Chemical Analyses
Details of the quality assurance procedures used to generate chemical concentrations
within both sediments and tissue samples with acceptable levels of precision and
33
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accuracy are given in U.S. EPA (2001 a). Briefly, a performance-based approach was
used, which depending upon the compound included 1) continuous laboratory
evaluation through the use of Certified Reference Materials (CRMs) and/or Laboratory
Control Materials (LCMs), 2) laboratory spiked sample matrices, 3) laboratory reagent
blanks, 4) calibration standards, and 5) laboratory and field replicates.
Control limit criteria for "relative accuracy" were based on comparing the laboratory's
value to the true or "accepted" values in CRMs or LCMs (see U.S. EPA, 2001 a for
details). The specific requirements for PAHs and PCBs/pesticides are that the "Lab's
value should be within ±30% of true value on average for all analytes; not to exceed
±35% of true value for more than 30% of individual analytes." (U.S. EPA 2001 a). In
addition to evaluating the individual PAH and PCB analytes, relative accuracy for total
PAHs and PCBs was determined for each combined group of organic compounds.
Metals and other inorganic compounds were treated individually, and the laboratory's
value for each analyte should be within ±20% of the true value of the CRM or LCM.
Because of inherent variability at low concentrations, these control limit criteria were
applied only to analytes having CRM or LCM values >10 times the MDL.
To evaluate precision, each laboratory periodically analyzed CRM or LCM samples
using a control limit of 3 standard deviations of the mean (Taylor, 1987). Based on
analysis of all the samples in a given year, an overall relative standard deviation (RSD,
or coefficient of variation) of less than 30% was considered acceptable precision for
analytes with CRM concentrations > 10 times the MDL.
In order to evaluate the MQOs for precision, various analytical quality assurance/quality
control (QA/QC) samples were used, field measurement procedures were followed, and
field vouchers were collected. For analytical purposes, Method Detection Limits
(MDL's) were calculated for the detection of each analyte at low levels distinguished
above background noise, taking into consideration the relative sensitivity of an analytical
method, based on the combined factors of instrument signal, sample size, and sample
processing steps. The MDL is defined as "the minimum concentration of a substance
that can be measured and reported with 99% confidence that the analyte concentration
is greater than zero and is determined from analysis of a sample in a given matrix
containing the analyte." (Code of Federal Regulations 40 CFR Part 136). Approved
laboratories were expected to perform in general accord with the target MDLs presented
for NCA analytes (US EPA, 2001 a, Table A7-2). Because of analytical uncertainties
close to the MDL, there is greater confidence with concentrations above the Reporting
Limit (RL), which is the concentration of a substance in a matrix that can be reliably
quantified during routine laboratory operations. Typically, RLs are 3 to 5 times the MDL.
Concentrations between the MDL and the RL were used in generating the CDF and
mean for the analyte. Values below the MDL were set to 0 and this value was used in
calculating both the CDFs and means.
34
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Table 2-6 lists the units, method detection limits (MDL), and reporting limits (RL) for
each compound measured in sediment samples. The analytical methods are those
used in the NOAA NS&T Program (Lauenstein and Cantillo, 1993) or documented in the
EMAP Laboratory Methods Manual (U.S. EPA, 1994b). The target MDLs for the
National Coastal Assessment (US EPA, 2001 a) were achieved in 92% of
sediment analytes in California (Table 2-6). Exceedances of the target MDL could
potentially affect the frequency with which a compound is detected, but would have little
effect on the shape of the CDF since such exceedances occur at the low end of the
concentration distribution.
Table 2-7 lists the units, method detection limits (MDL), and reporting limit (RL) for the
tissue analytes. The target MDLs for the National Coastal Assessment (US EPA,
2001 a) were achieved in 90% of tissue analytes (Table 2-7). As mentioned for the
sediments, exceedances of the target MDL could potentially affect the frequency with
which a compound is detected, but would have little effect on the shape of the CDF
since such exceedances occur at the low end of the concentration distribution.
Prior to analysis of 1999 field samples, state laboratories participating in the NCA
program performed a demonstration of capability using SRMs provided by EPA.
Results of this exercise are described in EPA (2004, Appendix A). Results were
deemed acceptable for California.
A post-analysis assessment of the success of the analytical laboratories in meeting
NCA QA/QC guidelines was conducted by the QA officer of the Western Ecology
Division. These results are summarized in Table 2-8. Accuracy of results as assessed
by comparison to either an SRM, CRM, or LCM was within guidelines for analysis of
metals in both sediment and tissues. For sediment PCBs and pesticides, the
performance of the California laboratories, while acceptable, was based on a limited
number of analytes in the LCM. Accuracy could not be assessed for the field samples
for pesticides because the laboratory did not analyze reference tissue material, although
ability to meet standards was demonstrated in the initial lab capability exercise.
35
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Table 2-6. Units, method detection limits (MDL), reporting limits (RL), analytical method,
and responsible laboratory for sediment chemistry. Target MDLs are from the National
Coastal Assessment (US EPA, 2001 a). NR = not reported. NA = not applicable.
Analyte
Aluminum
Antimony
Arsenic
Cadmium
Chromium
Copper
Iron
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Tin
Zinc
PCB (21 congeners)
DDT, ODD, and DDE
PAHs (21 compounds)
Aldrin
Alpha-Chlordane
Dieldrin
Endosulfan I
Endosulfan II
Endosulfan Sulfate
Endrin
Heptaclor
Heptachlor Epoxide
Units
(dry wt.)
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
Target
MDL
1500
0.2
1.5
0.05
5.0
5.0
500
1.0
1.0
0.01
1.0
0.1
0.05
0.1
2.0
1.0
1.0
10
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
CA
MDL/RL
0.05/0.15
0.002/0.006
0.1/0.3
0.002/0.006
0.03/0.09
0.03/0.09
2.0/6.0
0.002/0.006
0.003/0.009
0.015/0.045
0.006/0.018
0.002/0.006
0.008/0.024
0.002/0.006
0.02/0.06
1/5
1/5
5/13
1/5
2/5
1/5
5/10
5/10
5/10
5/10
1/5
1/5
Method
ICPMS
ICPMS
ICPMS
ICPMS
ICPMS
ICPMS
FAA
ICPMS
ICPMS
FIMS
ICPMS
HAA
GFAA
ICPMS
ICPMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
Laboratory
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG-WPCL
CDFG
CDFG
CDFG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
36
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Lindane (gamma-BHC)
Mi rex
Trans-Nonachlor
TOC
Percent fines
ng/g
ng/g
ng/g
percent
percent
1.0
1.0
1.0
NA
NA
2/5
2/5
1/5
0.01/0.01
NR
GCMS
GCMS
GCMS
MARPCN I
wet sieve
CRG
CRG
CRG
MLML
MLML
Analytical Methods: FAA = flame atomic absorption, GCMS = gas
chromatography/mass spectroscopy, FIMS = Flow Injection Mercury System, ICPMS =
Inductively Coupled Plasma-Mass Spectrometry , HAA = Hydride Atomic Absorption
Analysis, GFAA = graphite, furnace atomic absorption spectrometry, MARPCN I = High
temperature combustion method.
Analytical Laboratories: MLML = Moss Landing Marine Laboratory, CRG = CRG
Environmental Laboratories (Los Angeles, California), CDFG = California Dept. Fish and
Game , CDFG-WPCL = California Dept. Fish and Game - Water Pollution Control
Laboratory.
37
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Table 2-7. Units, method detection limits (MDL), reporting limits (RL), analytical method,
and responsible laboratory for tissue chemistry. Target MDLs are from the National
Coastal Assessment (US EPA, 2001 a). NA = not applicable.
Analyte
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
PCB (20 congeners)
PCB8, PCB 195
DDT, ODD, and DDE
Aldrin
Alpha-Chlordane
Dieldrin
Endosulfan I
Endosulfan II
Endosulfan Sulfate
Endrin
Heptaclor
Heptachlor Epoxide
Lindane (gamma-BHC)
Mi rex
Toxaphene
Units
(wet wt.)
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
Mg/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
ng/g
Target
MDL
10.0
2.0
0.2
0.1
5.0
0.1
0.01
0.05
1.0
0.5
50.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
CA
MDL/RL
0.012/0.036
0.025/0.075
0.0005/0.0015
0.007/0.021
0.007/0.021
0.0005/0.0015
0.005/0.015
0.0015/0.0045
0.025/0.075
0.002/0.006
0.005/0.015
1/2-5
1/2
1/5
1/2
1/2
2/4
1/2
1/2
5/10
2/4
5/10
2/4
5/10
2/4
5/10
10/20
Method
ICPMS
ICPMS
ICPMS
ICPMS
ICPMS
ICPMS
ICPMS
FIMS
ICPMS
ICPMS
ICPMS
ICPMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
GCMS
Laboratory
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CDFG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
CRG
38
-------
Trans-Nonachlor
% Moisture
ng/g
Mg/g
2.0
NA
1/5
NA
GCMS
conventional
oven
CRG
CDFG
Analytical Methods: FAA = flame atomic absorption, GCMS = gas
chromatography/mass spectroscopy, FIMS = Flow Injection Mercury System, ICPMS =
Inductively Coupled Plasma-Mass Spectrometry , HAA = Hydride Atomic Absorption
Analysis, GFAA = graphite, furnace atomic absorption spectrometry, MARPCN I = High
temperature combustion method.
Analytical Laboratories: MLML = Moss Landing Marine Laboratory, CRG = CRG
Environmental Laboratories (Los Angeles, California), CDFG = California Dept. Fish and
Game , CDFG-WPCL = California Dept. Fish and Game - Water Pollution Control
Laboratory.
39
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Table 2-8. Summary of performance of California analytical laboratories with regard to QA/QC criteria for analysis
of reference materials, matrix spike recoveries, and relative percent differences (RPD) of duplicates. MS = matrix
spike, SRM = Standard Reference Material, CRM = Certified Reference Material, LCM = Laboratory Reference
Material, NA = not analyzed.
Analyte Material
PAHs Sediment
Metals Sediment
Tissue
PCBs Sediment
Tissue
Pesticides Sediment
Tissue
Mean of all Less than 30% of analytes were within
analytes 35% of true value (% exceeding if >30%)
< ±30% SRM/CRM/LCM
(# analytes reported / # of analytes in
SRM/CRM/LCM)
Yes Yes LCM (15/22)
Yes Yes LCM (14/1 5)
Yes Yes LCM (11/1 3)
Yes Yes LCM (13/21)
Yes* YesCRM(8*/21)
Yes* Yes LCM (3*/20)
No no reference material used
Matrix spike
recovery within
50% -150%
NoMSs
? - no true
values**
? - no true
values**
NoMSs
Yes
NoMSs
Yes
RPDs
MS / non-zero duplicate samples
average <30%
NA/Yes
Yes/No sample dups
Yes/Yes
NA/no non-zeros
Yes/Yes
NA/no non-zeros
Yes/No (low values)
* Fewer than 50% of NCA analytes were present in LCM.
** Duplicate values, but not true values, were reported for matrix spikes by the analytical laboratory.
-------
2.4.2 QA of Taxonomy
Quality control of taxonomic identifications involved the establishment of a network of
secondary QA/QC taxonomic specialists who confirmed identifications made by the
primary taxonomists, and provided standardization of identifications among the state
participants.
In order to assure uniform taxonomy and nomenclature among the primary taxonomists
for each group, and to avoid problems with data standardization at the end of the
project, progressive QA/QC and standardization were implemented. At frequent,
regular intervals (i.e., monthly), as primary taxonomy was completed, vouchers, voucher
sheets, and a portion of the QA samples were sent to the QA taxonomists. Immediate
feedback from the QA taxonomists to the primary taxonomists was used to correct work
and standardize between regional taxonomists. Each voucher was accompanied by a
voucher sheet listing the following information: major taxon (e.g., Annelida); family;
genus; species; sample from which the specimen was taken; references used in the
identification; and any characteristics of the specimen that differ from the original
description. Provisional species were described in detail on the voucher sheet.
As voucher specimens and bulk samples were processed by the QA taxonomist, any
differences in identifications or counts were discussed and resolved with the primary
taxonomist. The original data set remained with the primary taxonomist, and changes
agreed upon between the primary and QA taxonomists were made by the primary
taxonomist on a copy of the original data set. Changes to the data based on QA/QC
analysis were tracked in writing by both the primary and QA taxonomists.
41
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Table 2-9. Listing of primary and QA/QC taxonomists by taxon and region for the 1999
Western Coastal EMAP study.
Organisms
Annelida
Arthropoda
Mollusca
Echinodermata
Miscellaneous taxa
Freshwater fauna
QA/QC
Taxon omist
Gene Ruff
Don Cadien
Don Cadien
Gordon Hendler
John Ljubenkov
Rob Plotnikoff/
Chad Wiseman
Primary
Taxonomists
John Oliver
Larry Lovell
Gene Ruff
Kathy Welch
Peter Slattery
Tony Phillips
Jeff Cordell
Peter Slattery
Kelvin Barwick
John Ljubenkov
Susan Weeks
Peter Slattery
Nancy Carder
Scott McEuen
Peter Slattery
John Ljubenkov
Scott McEuen
Not Applicable
Not Applicable
Jeff Cordell
Region*
NC
SC
WO
WO
NC
SC
WO
NC
NC
SC
WO
NC
SC
WO
NC
SC
WO
NC
SC
WO
*NC: Northern California, SC: Southern California, WO: Washington & Oregon
42
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2.5 Data Management
Data management for the West Coast stations sampled in 1999 is a component of the
overall EMAP Western Coastal Information Management Program. The Information
Management System is based on a centralized data storage model using standardized
data transfer protocols (SDTP) for data exchange among program participants. The data
are submitted to the Information Manager (IM) located at the Southern California Coastal
Water Research Project (SCCWRP) for entry into the relational database (Microsoft
Access 2000).
The data flow consists of interactions among four levels. Field crew leaders and
laboratory supervisors are responsible for compiling data generated by their
organizations and for entering the data into one or more of the SDTP tables. The State
Information Management (IM) Coordinator is responsible for compiling all data generated
within a state into a unified state database. The Western EMAP IM Coordinator is
responsible for working with State Coordinators to develop the SDTP, and for creation
and management of the centralized West Coast EMAP database. The EMAP IM
Coordinator, located at the Atlantic Ecology Division of EPA at Narragansett, Rhode
Island, is responsible for accepting data from Western EMAP, for placing it in the
national EMAP database, and for transferring it to other EPA databases, such as
STORET.
Once all data tables of a particular data type (e.g. all tables containing fish data) were
certified by the WIMC, integrated multi-state data tables were provided to the Western
EMAP Quality Assurance Coordinator (QAC). The QAC reviewed the data with respect
to scientific content. Necessary corrections resulting from this review process were
returned to the Western EMAP IM Coordinator who was responsible for working with the
State IM Coordinator to make necessary changes.
Following certification of all portions of the data by the QAC, the Western EMAP IM
Coordinator submitted the integrated multi-state data set to the EMAP IM Coordinator
who is the point of contact for data requests about the integrated data set.
Details of the Western EMAP Information Management process are provided in Cooper
(2000). The structure of each of the relational data base tables and supporting database
look up tables used by the states to submit data to the Western EMAP IM Coordinator
are provided in this document.
2.6 Unsamplable Area
All stations in California were visited. Among the base stations, there were no grab or
trawl samples obtained at CA99-3019 (Carmel Bay) or CA99-3024 (San Luis Obispo
Bay) because of rocky substrate at the sites. Site CA99-3027, located in the Ventura
River, was not sampled because the station location was actually located on land and
the adjacent aquatic habitat could not be sampled because it consisted of a large
43
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boulder substrate. Among the northern California intensification sites, no grab or trawl
samples were obtained at stations CA99-3056 (Wilson River) CA99-3058 (Klamath
River), CA99-3066 (Noyo River) CA99-3072 (Albion River), and CA99-3075 (Elk Creek)
because of the presence of rocky substrates. No trawl was obtained at station CA99-
3056 (Wilson River) because there was insufficient room to deploy gear.
44
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3.0 Indicator Results
3.1 Habitat Indicators
3.1.1 Water Depth at Sample Sites
Bottom depth, corrected for tidal stage and referenced to MLLW, for sample stations for
the California small estuaries, ranged from -29.3 m to 1.0 m across all 50 sites in the
base study. The 90th percentile of area of the California small estuaries had a water
depth 0.3 m below MLLW (Figure 3.1 -1). Only 3.3% of the estuarine area represented
by the 1999 sample frame was > 0 m, i.e. above MLLW. In contrast, bottom depth in
the Northern California rivers ranged only between - 4.8 m and 1.4 m relative to MLLW.
The 90th percentile of area of the Northern California rivers had a bottom depth
approximately 1 m above MLLW (Figure 3.1-2). Nearly 45 % of estuarine area of the
Northern California rivers was above MLLW (> 0 m).
3.1.2 Salinity
Salinity in the bottom water for the California small estuaries ranged from 0.4 psu to
33.8 psu across all 50 sites in the base study. The 90th percentile of area of the small
estuaries had a salinity of 32.9 psu (Figure 3.1-3). About 93% of the area of the
California estuaries would be classified as euhaline (> 30 psu) based on the EMAP
sampling. The extended left tail of the CDF indicates that a few samples were taken at
low salinities, but that these sites constituted a small percentage of the total estuarine
area. The intensification sites in the Northern California rivers tended to have lower
salinities, although the range was comparable to the rest of the state (Figure 3.1-4).
While the 90th percentile of area of the Northern California rivers had a value of 32.4
psu, approximately 49% of the area of the Northern California rivers had salinity less
than 20 psu, and 18% of the area of the Northern California rivers had salinity less than
3 psu. In interpreting these results, it is important to recognize that salinity can vary
both tidally and seasonally, as well as with depth in the water column, and that these
single measurements are "snapshots" during the sampling events.
3.1.3 Water Temperature
Temperature in the bottom water for the California small estuaries ranged from 10.1 °C
to 32.1 °C across all 50 sites in the base study. The relatively wide range of bottom
water temperature values reflects the two biogeographic provinces which were sampled
in California. The range of surface water temperatures was very similar to that for
bottom water temperatures (13.5 °C to 32.1 °C). Within a station, the maximum
temperature difference between surface and bottom waters was 5.4 °C, observed at a
station in Long Beach Harbor. Approximately 17% of the area of the small estuaries had
a temperature at the bottom > 20 °C, with a similar percentage of area having bottom
water temperatures < 11 °C (Figure 3.1-5). The Northern California rivers (Figure 3.1-
45
-------
6) showed a narrower range of bottom water temperatures from 11.6 °C to 21.9 °C.
These temperatures are representative of summer conditions in the region.
3.1.4 pH
The pH of bottom waters for the California small estuaries ranged from 6.9 to 9.5
across all 49 sites in the base study with pH data. The range for pH in surface water
samples was identical to that for bottom waters. The 90th percentile of area of the small
estuaries had a bottom water pH of 8.1 (Figure 3.1-7), with the 90th percentile of area of
the Northern California rivers having a bottom water pH of 8.3 (Figure 3.1-8). The
Northern California rivers showed a slightly wider range of bottom water pH from 6.6 to
10.2. Values of pH > 9 tended to be found at sites with low salinity (< 7 psu), with the
exception of the station from Point Mugu Lagoon where a bottom water pH of 9.3 and a
salinity of 33.4 psu were recorded.
3.1.5 Sediment Characteristics
The percent silt-clay of sediments ranged from 0.9 % to 96.42 % at the 47 stations
within the base study from which soft sediment samples could be obtained (Figure 3.1-
9). About 39% of the area of the California small estuaries had sediments composed of
sands (< 20 % silt-clay), about 46 % was composed of intermediate muddy sands (20-
80 % silt-clay), and about 15 % was composed of muds (>80 % silt-clay). The Northern
California rivers had relatively greater proportions of estuarine area characterized by
sands (68%), and less area characterized by muds (4%) or intermediate muddy sands
(32%) (Figure 3.1-10).
Percent total organic carbon (TOC) in sediments ranged from 0.02 % to 7.4 % at the 47
stations within the base study from which soft sediment samples could be obtained
(Figure 3.1-11). The 90th percentile of area of both the California small estuaries and
the Northern California rivers had a sediment TOC level of 1.3 %. However, reflecting
the generally sandier nature of sediments in these estuaries, the range of TOC values
was only 0.12 % to 2.8 % at the 26 stations within Northern California rivers sampled for
TOC (Figure 3.1-12).
3.1.6 Water Quality Parameters
Water quality parameters are presented as water column mean values based on the
concentration averaged over the surface, mid-water, and bottom water samples.
Chlorophyll a
The average water column concentration of chlorophyll a in California small estuaries
(Figure 3.1-13) ranged from 0.47 to 47.59 ug L"1 across all 50 sites where chlorophyll
measurements were collected. The 90th percentile of area in California small estuaries
had a chlorophyll a concentration of 5.7 ug L"1. Chlorophyll a concentration within the
46
-------
Northern California rivers (Figure 3.1-14) ranged between 0.42 and 25.7 ug L~1, while
the 90th percentile of area had a chlorophyll a concentration of 3.1 ug L~1.
Nutrients
The average water column concentration of nitrate in California small estuaries (Figure
3.1-15) ranged from 3.4 to 3404 ug L"1, with the 90th percentile of area characterized by
a nitrate concentration of 242 ug L"1. Less than 0.5% of estuarine area exceeded
concentrations of 1900 ug L"1. Nitrate concentration within the Northern California rivers
(Figure 3.1-16) ranged between 0 and 440 ug L"1, with the 90th percentile of area
characterized by a nitrate concentration of 231 ug L"1.
The average water column concentration of nitrite in California small estuaries (Figure
3.1-17) ranged from 0 to 79.6 ug L"1, with the 90th percentile of total estuarine area
characterized by a nitrite concentration of 24 ug L"1. Nitrate concentration within the
Northern California rivers (Figure 3.1-18) was within the similar range of 0 to 50 ug L"1,
with the 90th percentile of total area characterized by a nitrite concentration of 40 ug L"1.
The average water column concentration of ammonium in California small estuaries
(Figure 3.1-19) ranged from 3.4 to 150 ug L"1, with the 90th percentile of total estuarine
area characterized by an ammonium concentration of 80 ug L"1. Ammonium
concentration within the Northern California rivers (Figure 3.1-20) ranged from 0 to 370
ug L"1, with the 90th percentile of total estuarine area characterized by an ammonium
concentration of 74 ug L"1. Approximately 0.06% of estuarine area in Northern
California rivers was characterized by water column ammonium concentrations > 300
M9 L1.
The average water column concentration of total dissolved nitrogen in California small
estuaries (Figure 3.1-21) ranged from 9.7 to 3518.8 ug L"1, with the 90th percentile of
total estuarine area characterized by a total nitrogen concentration of 293 ug L"1. Total
nitrogen concentration within the Northern California rivers (Figure 3.1-22) ranged from
30 to 600 ug L"1, with the 90th percentile of total estuarine area characterized by a water
column total nitrogen concentration of 293 ug L"1.
The average water column concentration of orthophosphate in California small estuaries
(Figure 3.1-23) ranged from 0 to 220.0 ug L1, with the 90th percentile of total estuarine
area characterized by a concentration of 48 ug L"1. Orthophosphate concentration
within the Northern California rivers (Figure 3.1-24) ranged between 0 and 68.5 ug L"1,
with the 90th percentile of area characterized by a concentration of 49 ug L"1.
The ratio of total nitrogen (nitrogen as nitrate + nitrite + ammonium) concentration to
total orthophosphate concentration was calculated as an indicator of which nutrient may
be controlling primary production in west coast small estuaries. A ratio above 16 is
generally considered indicative of phosphorus limitation, and a ratio below 16 is
considered indicative of nitrogen limitation (Geider and La Roche, 2002). The N/P ratio
47
-------
(Figure 3.1-25) ranged from 1.1 to 393.5, across the 49 California small estuary
stations where sufficient measurements were collected to compute the ratio.
Approximately 69% of estuarine area had N/P values < 16, while the 90th percentile of
area had a ratio of 23.3. The long right hand tail of the CDF was due to two stations
representing less than 0.3 % of estuarine area with N/P ratios > 100. The N/P ratio
(Figure 3.1-26) ranged from 4.5 to 149.3, across the 23 Northern California rivers
where sufficient measurements were collected to compute the ratio. Approximately 76
% of estuarine area in Northern California rivers had N/P values < 16, while the 90th
percentile of area also had a ratio of 23.3. The long right hand tail of the CDF was due
to two stations representing less than 0.2 % of estuarine area with N/P ratios > 67.
Total Suspended Solids
The average water column concentrations of total suspended solids (TSS) in California
small estuaries (Figure 3.1-27) ranged from 0.5 to 276.2 mg L1, with the 90th percentile
of total estuarine area characterized by a TSS concentration of 19 mg L"1. TSS
concentration within the Northern California rivers (Figure 3.1-28) ranged between 0
and 60.7 mg L"1, with the 90th percentile of total estuarine area characterized by a TSS
concentrations of 14.5 mg L1.
Percent Light Transmission
The percent light transmission of the water column (adjusted to a reference sample
depth of 1 m) in California small estuaries (Figure 3.1-29) ranged from 1.5 to 73.4
percent. Approximately 23 % of total estuarine area showed a light transmission of < 20
% of surface illumination at a depth of 1 m, while approximately 8% of estuarine area
had a light transmission of < 10% at 1 m. Light transmission within the Northern
California rivers (Figure 3.1-30) ranged between 1.8 and 59 percent. Approximately 53
% of total estuarine area showed a percent light transmission of < 20 % of surface
illumination at a depth of 1 m, while approximately 4% of estuarine area had a light
transmission of < 10% at 1 m.
Secchi Depth
The secchi depth of the water column in California small estuaries (Figure 3.1-31)
ranged from 0.4 to 17 m. The 90th percentile of total estuarine area showed a secchi
depth of 5.6 m. The water depths in the Northern California rivers were too shallow to
obtain measurements of secchi depth in 28 of 30 cases, and these data were not
analyzed.
3.1.7 Water Column Stratification
As an indicator of water column stratification, two indices were calculated for with
temperature and salinity data. The first index was the simple difference between bottom
and surface salinities. The second index (Aot) was the difference between the
48
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computed bottom and surface ot values, where ot is the density of a parcel of water with
a given salinity and temperature relative to atmospheric pressure. Results of the two
indices were extremely similar.
For the California small estuaries, the simple stratification index ranged only between -
0.2 and 0.7. Less than 10 % of estuarine area showed index values < 0, indicating
bottom waters less saline than surface waters (Figure 3.1-32). There was little indication
of water column stratification for the California small estuaries. For the Northern
California rivers, the stratification index ranged from -0.1 to 5.2, although 97 % of
estuarine area had index values < 0.4 (Figure 3.1-33).
The Aot index had values ranging from -0.005 to +1.68. Approximately 4% of California
small estuary area showed Aot index values < 0, indicating bottom waters less saline
than surface waters (Figure 3.1-34). No sites had Aot index values > 2, indicating
strong stratification. Approximately 5% of the area of Northern California rivers showed
Aot index values < 0, indicating bottom waters less saline than surface waters (Figure
3.1-35). Approximately 3% of estuarine area had Aot index values > 2, indicating strong
stratification.
The limited indication of strong water column stratification within the California small
estuaries or Northern California rivers sampled is consistent with the large tidal
amplitude across much of the region, which should lead to a high degree of water
column mixing. Additionally the sampling period is during the summer period of low
rainfall and low freshwater runoff which should also reduce the extent of vertical
stratification during the sample period.
49
-------
MLLW Corrected Bottom Depth
California Small Estuaries
100 -
Z
< 80
3
3
o
60 -
40 -
20 -
-35 -30 -25 -20 -15 -10 -5 0
Water Depth Relative to MLLW (m)
Figure 3.1-1. Percent area (and 95% C.I.) of California small estuaries vs. MLLW
corrected bottom depth.
MLLW Corrected Bottom Depth
Northern California Rivers
100 -
re
Si
< 80
S. 60
.1
*•«
1 40 H
I
o
20 -
-4 -3 -2 -1 0
Water Depth Relative to MLLW (m)
Figure 3.1-2. Percent area (and 95% C.I.) of Northern California rivers vs. MLLW
corrected bottom depth.
50
-------
Bottom Salinity
California Small Estuaries
*-
I
Ol
IS
3
E
3
o
100 -
80 -
60 -
40 -
20 -
^ i j.- 1-1 j.
yo /o uontioence interval
£
J
10 15 20 25
Salinity
30 35
40
Figure 3.1-3. Percent area (and 95% C.I.) of California small estuaries vs. salinity of
bottom waters.
Bottom Salinity
Northern California Rivers
100 -
ro
<
Ol
o
I
80 -
60 -
J2 40 -
|
O 20 -
10 15 20 25
Salinity
30 35
40
Figure 3.1-4. Percent area (and 95% C.I.) of Northern California rivers vs. salinity of
bottom waters.
51
-------
Bottom Temperature
California Small Estuaries
100 -
c
01
u
S. 60
•= 40 -
3
o
20 -
-Cumulative Percent
- 95% Confidence Interval
10 15 20
Degrees (C)
25
30
35
Figure 3.1-5. Percent area (and 95% C.I.) of California small estuaries vs. temperature
of bottom waters.
Bottom Temperature
Northern California Rivers
100 -
< 80 -
60 -
40 -
20 -
-Cumulative Percent
-95% Confidence Interval
10 15
Degrees (C)
20
25
Figure 3.1-6. Percent area (and 95% C.I.) of Northern California rivers vs. temperature
in bottom waters.
52
-------
100 -
HI
< 80
HI
u
s. 60
•5 40
3
o
20 -
Bottom pH
California Small Estuaries
-Cumulative Percent
-95% Confidence Interval
PH
10
Figure 3.1-7. Percent area (and 95% C.I.) of California small estuaries vs. pH in bottom
waters.
Bottom pH
Northern California Rivers
100 -
< 80 -
60 -
•^ 40 -
3
O
20 -
-Cumulative Percent
-95% Confidence Interval
6
PH
10
12
Figure 3.1-8. Percent area (and 95% C.I.) of Northern California rivers vs. pH in bottom
waters.
53
-------
Percent Silt-Clay Content
California Small Estuaries
100 -
40 -
20 -
95% Confidence Interval
T
20
40 60
Percent Silt-Clay
100
120
Figure 3.1-9. Percent area (and 95% C.I.) of California small estuaries vs. percent silt-
clay of sediments.
Percent Silt-Clay Content
Northern California Rivers
100 -
1
40 -
20 -
0 4-
Cumulative Percent
- 95% Confidence Interval
0 10 20 30
40 50 60 70 80 90
Percent Silt-Clay
100
Figure 3.1-10. Percent area (and 95% C.I.) of Northern California rivers vs. percent silt-
clay of sediments.
54
-------
Percent Total Organic Carbon
California Small Estuaries
— Cumulative Percent
• - 95% Confidence Interval
345
Percent Silt-Clay
Figure 3.1-11. Percent area (and 95% C.I.) of California small estuaries vs. percent
total organic carbon of sediments.
Percent Total Organic Carbon
Northern California Rivers
100 -
60 -
•3 40
|
O
20 -
Cumulative Percent
95% Confidence Interval
0.5
1 1.5 2
Percent Silt-Clay
2.5
Figure 3.1-12. Percent area (and 95% C.I.) of Northern California rivers vs. percent
total organic carbon of sediments.
55
-------
Water Column Chlorophyll a Concentration
California Small Estuaries
100 -
"
HI
o
HI
Q.
HI
40 -
20 -
r^ i i- n j.
- - -95% Confidence Interval
10 20 30
Concentration (ug/L)
40
50
Figure 3.1-13. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean concentration of chlorophyll a.
Water Column Chlorophyll a Concentration
Northern California Rivers
100 -
80 -
3 40 -
E
O
20 -
-Cumulative Percent
-95% Confidence Interval
10 15 20
Concentration (ug/L)
25
30
Figure 3.1-14. Percent area (and 95% C.I.) of Northern California rivers vs. water
column concentration of chlorophyll a.
56
-------
Water Column Nitrate Concentration
California Small Estuaries
100 -
HI
Q.
60 -
40 -
20 -
-Cumulative Percent
- - - - -95% Confidence Interval
500 1000 1500 2000 2500 3000
Concentration (ug/L)
3500 4000
Figure 3.1-15. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean nitrate concentration.
Water Column Nitrate Concentration
Northern California Rivers
100 -
HI
u
80 -
60 -
•5 40
E
o
20 -
100 200 300
Concentration (ug/L)
400
500
Figure 3.1-16. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean nitrate concentration.
57
-------
Water Column Nitrite Concentration
California Small Estuaries
100 -
re
| 8o^
« 60-|
40 -
20 -
-•'/
-Cumulative Percent
- 95% Confidence Interval
10 20 30 40 50 60
Concentration (ug/L)
70
80
90
Figure 3.1-17. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean nitrite concentration.
Water Column Nitrite Concentration
Northern California Rivers
100 -
<
3 40
E
3
O
20 -
-Cumulative Percent
- 95% Confidence Interval
10 20 30 40
Concentration (ug/L)
50
60
Figure 3.1-18. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean nitrite concentration.
58
-------
Water Column Ammonium Concentration
California Small Estuaries
100 -
Z
< 80
O
60 -
20 -
..-Jf
20 40 60 80 100
Concentration (ug/L)
120 140
160
Figure 3.1-19. Percent area (and 95% C.I.) of California small estuaries vs. water
column ammonium concentration.
Water Column Ammonium Concentration
Northern California Rivers
100 -
< 80
-------
Mean Total Dissolved Nitrogen Concentration
California Small Estuaries
100 -
HI
Q.
HI
>
60 -
"5 40 -
|
O
20 -
-Cumulative Percent
• 95% Confidence Interval
500 1000 1500 2000 2500
Concentration (ug/L)
3000
3500
4000
Figure 3.1-21. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean total nitrogen (nitrate + nitrite + ammonium) concentration.
Mean Total Dissolved Nitrogen Concentration
Northern California Rivers
100 -
u
Q.
HI
>
is
3
3
o
80 -
40 -
20 -
100 200 300 400 500
Concentration (ug/L)
600
700
Figure 3.1-22. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean total nitrogen (nitrate + nitrite + ammonium) concentration.
60
-------
Water Column Orthophosphate Concentration
California Small Estuaries
100 -
c
HI
o
HI
Q.
HI
>
is
3
3
o
80 -
40 -
20 -
-Cumulative Percent
- 95% Confidence Interval
100 200 300 400
Concentration (ug/L)
500
600
Figure 3.1-23. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean Orthophosphate concentration.
Water Column Orthophosphate Concentration
Northern California Rivers
100 -
u
Q.
HI
>
is
3
3
O
80 -
40 -
20 -
-
r^ i i- n j.
_ _ _ -95% Confidence Interval
50 100 150
Concentration (ug/L)
200
250
Figure 3.1-24. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean Orthophosphate concentration.
61
-------
Water Column Molar N/P Ratio
California Small Estuaries
100 -
re
HI
< 80-
1:
HI
u
» 60 -
Q.
HI
^
•= 40 -
3 tu
3
O
20 -
C
#
'/•'
|j
•
\
jE
ft
i"t
Jn
ji ^^^^^^ Cumulstive Percent
M ' ----- 95% Confidence Intervsl
r
\i
i
50 100 150 200 250 300 350 400 45
Ratio
Figure 3.1-25. Percent area (and 95% C.I.) of California small estuaries vs. water
column mean ratio of total nitrogen (nitrate + nitrite + ammonium) concentration
to total orthophosphate concentration.
Water Column Molar N/P Ratio
Northern California Rivers
100 -
< 80 -
1:
HI
u
d) 6
Q.
HI
= 40-1
O
20 -
-Cumulative Percent
- 95% Confidence Interval
20
40
80 100
Ratio
120
140
160
Figure 3.1-26. Percent area (and 95% C.I.) of Northern California rivers vs. water
column mean ratio of total nitrogen (nitrate + nitrite + ammonium) concentration
to total orthophosphate concentration.
62
-------
Water Column Total Suspended Solids Concentration
California Small Estuaries
.
r^ i i- n j.
.... 950/0 confidence Interval
50 100 150 200
Concentration (mg/L)
250
300
Figure 3.1-27. Percent area (and 95% C.I.) of California small estuaries vs. water
column total suspended solids concentration.
Water Column Total Suspended Solids Concentration
Northern California Rivers
100 -
<
"E
HI
u
HI
Q.
HI
80 -
40 -
20 -
10 20 30 40 50
Concentration (mg/L)
60
70
Figure 3.1-28. Percent area (and 95% C.I.) of Northern California rivers vs. water
column total suspended solids concentration.
63
-------
Percent Light Transmission at 1 m
California Small Estuaries
100 -
u
Q.
]f 40
3
5 20
10 20 30 40 50 60
Percent Light Transmission
70 80
Figure 3.1-29. Percent area (and 95% C.I.) of California small estuaries vs. percent
light transmission at a reference depth of 1 m.
Percent Light Transmission at 1 m
Northern California Rivers
HI
£> 60-
01
Q.
HI
If 40
3
o
20 -
r--'
10 20 30 40 50
Percent Light Transmission
70
Figure 3.1-30. Percent area (and 95% C.I.) of Northern California rivers vs. percent light
transmission at a reference depth of 1 m.
64
-------
Seechi Depth
California Small Estuaries
100 -
< 80
'c
u
$ 60
I
*j
JO
3
3
o
40 -
20 -
6 8 10 12
Secchi Depth (m)
14 16
18
Figure 3.1-31. Percent area (and 95% C.I.) of California small estuaries vs. water
column Secchi depth.
65
-------
Stratification Index
California Small Estuaries
-0.3
-0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
Bottom Salinity Minus Surface Salinity
Figure 3.1-32. Percent area (and 95% C.I.) of California small estuaries vs. water
column stratification index.
Stratification Index
Northern California Rivers
100 -
™
3
3
o
40 -
20 -
-Cumulative Percent
•95% Confidence Interval
01234
Bottom Salinity Minus Surface Salinity
Figure 3.1-33. Percent area (and 95% C.I.) of Northern California rivers vs. water
column stratification index.
66
-------
Aa,
California Small Estuaries
100 -
HI
g 60
HI
Q.
HI
>
If 40
3
o
0
-0.2 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.1
(at bottom - at surface)
Figure 3.1-34. Percent area (and 95% C.I.) of California small estuaries vs. Aot
stratification index.
Aa,
Northern California Rivers
100 -
HI
g 60
HI
Q.
HI
>
|S 40
3
O
-Cumulative Percent
•95% Confidence Interval
-0.5 0 0.5 1 1.5 2 2.5
(at bottom - at surface)
3.5
Figure 3.1-35. Percent area (and 95% C.I.) of Northern California rivers vs. Aot
stratification index.
67
-------
3.2 Exposure Indicators
3.2.1 Dissolved Oxygen
Dissolved oxygen (DO) concentrations in the bottom water for the California small
estuaries ranged from 3.75 mg/L to 16.29 mg/L, across the 50 stations where dissolved
oxygen concentrations were measured. Approximately 7% of estuarine area had a
bottom water DO concentration < 5 mg/L, while approximately 90% of the area of
California small estuaries had bottom water DO concentrations > 5.1 mg/L (Fig. 3.2 -1).
Dissolved oxygen (DO) concentrations in the bottom water for the Northern California
small estuaries had a somewhat smaller range, from 5.8 mg/L to 12.9 mg/L, across the
30 stations where dissolved oxygen concentrations were measured. One hundred
percent of the area of Northern California rivers had bottom water DO concentrations >
5 mg/L (Fig. 3.2 -2).
The range of dissolved oxygen (DO) concentrations in the surface waters of California
small estuaries was very similar to that for bottom waters (4.25 mg/L to 16.29 mg/L; Fig.
3.2 -3). Only approximately 0.2 % of the area of California small estuaries had surface
DO concentrations < 5 mg/L. Dissolved oxygen (DO) concentrations in the surface
water for the Northern California rivers had a somewhat smaller range, from 5.95 mg/L
to 13.5 mg/L, across the 30 stations where dissolved oxygen concentrations were
measured. One hundred percent of the area of Northern California rivers had surface
water DO concentrations > 5 mg/L (Fig. 3.2 -4).
3.2.2 Sediment Contaminants
3.2.2.1 Sediment Metals
Concentrations of sediment metals were measured at 47 stations in the California small
estuaries and in 26 stations in the Northern California rivers. The mean concentration
of each metal was calculated with the non-detects (i.e., less than the MDL) set to 0 (see
Table 2.7 for the MDL's). For comparative purposes, mean concentrations of metals
were also calculated using the subset of samples in which the metals were detected
(Table 3.2-1).
Arsenic
Arsenic was detected at all 47 of the California small estuary stations. Arsenic
averaged 3.5 ug/g at these stations with a maximum concentration of 17.1 ug/g in the
Los Angeles Harbor (Table 3.2-1). Fifty percent of the area of the California small
estuaries had an arsenic concentration less than 7.7 ug/g and 90% of the area had
concentrations less than 11.2 ug/g (Figure 3.2-5). Arsenic was also detected at all 26
Northern California river stations. Arsenic averaged 6.9 ug/g at these stations with a
maximum concentration of 10.8 ug/g in Wilson Creek (Table 3.2-2). Fifty percent of the
68
Continued on page 71
-------
Bottom Dissolved Oxygen Concentration
California Small Estuaries
100 -
c
0)
u
s. 60
3 **
E
3
o
20 -
-Cumulative Percent
- 95% Confidence Interval
4 6 8 10 12 14 16
Dissolved Oxygen Concentration (mg/L)
18
Figure 3.2 -1. Percent area (and 95% C.I.) of California small estuaries vs. dissolved
oxygen of bottom waters.
Bottom Dissolved Oxygen Concentration
Northern California Rivers
100 -
c
01
u
S. 60
•= 40 -
3
O
20 -
-Cumulative Percent
-95% Confidence Interva
2 4 6 8 10 12
Dissolved Oxygen Concentration (mg/L)
14
Figure 3.2 -2. Percent area (and 95% C.I.) of Northern California rivers vs. dissolved
oxygen of bottom waters.
69
-------
Surface Dissolved Oxygen Concentration
California Small Estuaries
100 -
80 -
60 -
3 40
3
O
20 -
.J—P
4 6 8 10 12 14
Dissolved Oxygen Concentration (mg/L)
16
18
Figure 3.2 -3. Percent area (and 95% C.I.) of California small estuaries vs. dissolved
oxygen of surface waters.
Surface Dissolved Oxygen Concentration
Northern California Rivers
100 -
80 -
60 -
3 40
3
O
20 -
4 6 8 10 12
Dissolved Oxygen Concentration (mg/L)
16
Figure 3.2 -4. Percent area (and 95% C.I.) of Northern California rivers vs. dissolved
oxygen of surface waters.
70
-------
area of the Northern California rivers had concentrations of 6.6 |jg/g or less while 90%
of the area had concentrations less than 8.3 |jg/g (Figure 3.2-6). Arsenic concentrations
exceeded the ERL at 18 California small estuary stations (46% of area) and at 7
Northern California river stations (22% of area), while no stations had values exceeding
the ERM (Table 3.2-1, 3.2-2).
Cadmium
Cadmium was detected at all 47 California small estuary stations. Cadmium averaged
0.36 ug/g at these stations with a maximum concentration of 4.3 ug/g in the Los
Angeles Harbor (Table 3.2-1). In comparison, no other station in the California small
estuaries or in the Northern California rivers had a concentration >1 ug/g. Fifty percent
of the area of California small estuaries had cadmium concentrations less than 0.20
ug/g and 90% of the area had concentrations less than 0.52 ug/g (Figure 3.2-7).
Cadmium was also detected at all 26 Northern California river stations. Cadmium
averaged 0.08 ug/g at these stations with a maximum of 0.21 ug/g in the Klamath River
(Table 3.2-2). Fifty percent of the area of the Northern California rivers had cadmium
concentrations less than 0.09 ug/g and 90% of the area had concentrations less than
0.19 ug/g (Figure 3.2-8). Cadmium concentrations exceeded the ERL only at 1
California small estuary station (0.1% of area), while no stations had values exceeding
the ERM (Tables 3.2-1, 3.2-2).
Chromium
Chromium was detected at all 47 California small estuary stations. Chromium averaged
143.3 ug/g in these stations with a maximum concentration of 927 ug/g in Drakes Bay
(Table 3.2-1). The only other concentration in the California small estuary stations >400
ug/g was the 907 ug/g value in Morro Bay. Fifty percent of the area of the California
small estuaries had concentrations less than 102.7 ug/g and 90% of the area had
concentrations less than 368.3 ug/g (Figure 3.2-9). Chromium was also detected at all
26 Northern California river stations. Chromium averaged 317 ug/g in the Northern
California rivers (Table 3.2-2) with the two highest concentrations of 1770 and 1250
ug/g both occurring in the Smith River. These were the only concentrations in either the
California small estuary stations or in the Northern California river stations >1000 ug/g.
Fifty percent of the area of the Northern California rivers had chromium concentrations
less than 267.0 ug/g and 90% had concentrations less than 1139.0 ug/g (Figure 3.2-
10). Chromium concentrations exceeded the ERL at 21 California small estuary
stations (58% of area), while 4 stations (9% of area) had values exceeding the ERM
(Table 3.2-1). Chromium concentrations exceeded the ERL at 16 Northern California
river stations (80% of area), while 6 stations (34% of area) had values exceeding the
ERM (Table 3.2-2).
Copper
Copper was detected at all 47 California small estuary stations. Copper averaged 35.1
ug/g in these stations with a maximum concentration of 398 ug/g in the Los Angeles
Harbor (Table 3.2-1). The only other concentration >100 ug/g was the 156 ug/g value in
Santa Barbara Harbor. Fifty percent of the area of the California small estuaries had
71
-------
concentrations less than 21.7 |jg/g and 90% of the area had concentrations less than
68.0 |jg/g (Figure 3.2-11). Copper was also detected at all 26 Northern California
stations. Copper averaged 17.8 ug/g in the Northern California river stations with a
maximum concentration of 43.6 ug/g in the Albion River (Table 3.2-2). Fifty percent of
the area of the Northern California rivers had concentrations less than 15.8 ug/g and
90% of the area had concentrations less than 39.1 ug/g (Figure 3.2-12). Copper
concentrations exceeded the ERL at 15 California small estuary stations (32% of area),
while 1 stations (0.3% of area) had values exceeding the ERM (Table 3.2-1). Copper
concentrations exceeded the ERL at 5 Northern California river stations (23% of area),
while no stations had values exceeding the ERM (Table 3.2-2).
Lead
Lead was detected at all 47 California small estuary stations. Lead averaged 25.9 ug/g
in these stations with a maximum concentration of 293 ug/g in the Los Angeles Harbor
(Table 3.2-1). No other station had concentrations >100 ug/g. Fifty percent of the area
of the California small estuaries had concentrations less than 12.9 ug/g and 90% of the
area had concentrations less than 39.8 ug/g (Figure 3.2-13). Lead was also detected at
all 26 Northern California river stations. Lead averaged 9.3 ug/g in the Northern
California river stations with a maximum concentration of 33.5 ug/g in the Albion River
(Table 3.2-2). Fifty percent of the area of the Northern California rivers had
concentrations less than 8.3 ug/g and 90% of the area had concentrations less than
11.3 ug/g (Figure 3.2-14). Lead concentrations exceeded the ERL at 5 California small
estuary stations (8% of area), and 1 station (0.3% of area) had a value exceeding the
ERM (Table 3.2-1). No Northern California river stations exceeded either the ERL or
ERM for lead (Table 3.2-2).
Mercury
Mercury was detected at 39 of the 47 (83%) California small estuary stations. Mercury
averaged 0.17 ug/g in the California small estuaries with a maximum concentration of
2.33 ug/g in the Los Angeles Harbor (Table 3.2-1). No other station in the California
small estuaries had a concentration >1 ug/g. Fifty percent of the area of the California
small estuaries had concentrations less than 0.09 ug/g and 90% of the area had
concentrations less than 0.34 ug/g (Figure 3.2-15). Mercury was detected at 25 of the
26 (96%) Northern California river stations. Mercury averaged 0.23 ug/g in the Northern
California rivers with a maximum concentration of 3.11 ug/g in the Estero Americano,
which empties into Bodega Bay (Table 3.2-2). The only other concentration >1 ug/g in
the Northern California rivers was the 1.37 ug/g value in the Albion River. Fifty percent
of the area of the Northern California rivers had concentrations less than 0.03 ug/g and
90% of the area had concentrations less than 0.36 ug/g (Figure 3.2-16). Mercury
concentrations exceeded the ERL at 15 California small estuary stations (42% of area),
while 1 station (0.3% of area) had a value exceeding the ERM (Table 3.2-1). Mercury
concentrations exceeded the ERL at 2 Northern California river stations (20% of area),
while 2 stations (9% of area) had values exceeding the ERM (Table 3.2-2).
72
-------
Nickel
Nickel was detected at all 47 California small estuary stations. Nickel averaged 32.1
ug/g in these stations with a maximum concentration of 116 ug/g in Arcata Bay (Table
3.2-1). Fifty percent of the area of the California small estuaries had concentrations
less than 24.1 ug/g and 90% of the area had concentrations less than 88.8 ug/g (Figure
3.2-17). Nickel was detected at all 26 Northern California river stations. Nickel
averaged 93.8 ug/g in the Northern California rivers with maximum concentrations of
354 and 307 ug/g in the Smith River (Table 3.2-2). The other three concentrations in
the Smith River were all >200 ug/g. Fifty percent of the area of the Northern California
rivers had concentrations less than 128.4 ug/g and 90% of the area had concentrations
less than 292.3 ug/g (Figure 3.2-18).
Nickel concentrations exceeded the ERL at 23 California small estuary stations (54% of
area), while 8 stations (22% of area) had values exceeding the ERM (Table 3.2-1).
Nickel concentrations exceeded the ERL at 18 Northern California river stations (81% of
area), while 12 stations (68% of area) had values exceeding the ERM (Table 3.2-2).
Nickel concentrations in relation to the published ERM values should be interpreted
cautiously since the ERM value has a low reliability (Long et al., 1995). Because of its
unreliability, nickel was excluded from a recent evaluation of sediment quality in
southern Puget Sound (Long et al., 2000). Additionally, a study of metal concentrations
in cores on the West Coast determined an historical background concentration of nickel
in the range of 35 - 70 ppm (Lauenstein et al., 2000), which brackets the value of the
ERM(51.6ppm).
Selenium
Selenium was detected at 43 of the 47 (91 %) California small estuary stations.
Selenium averaged 0.28 ug/g in the California small estuary stations with a maximum
concentration of 1.6 ug/g in the Los Angeles Harbor (Table 3.2-1). No other station in
the California small estuaries had a concentration >1 ug/g. Fifty percent of the area of
the California small estuaries had selenium concentrations less than 0.17 ug/g and 90%
of the area had concentrations less than 0.44 ug/g (Figure 3.2-19). Selenium was
detected in 22 of the 26 (85%) Northern California river stations. Selenium averaged
0.12 ug/g in the Northern California river stations with a maximum concentration of 0.39
ug/g in the Klamath River (Table 3.2-2). Fifty percent of the area of the Northern
California rivers had concentrations less than 0.13 ug/g and 90% of the area had
concentrations less than 0.33 ug/g (Figure 3.2-20). No stations exceeded either the
ERL or ERM for selenium (Tables 3.2-1, 3.2-2).
Silver
Silver was detected at all 47 California small estuary stations. Silver averaged 0.20
ug/g in these stations with a maximum concentration of 1.13 ug/g in the Los Angeles
Harbor (Table 3.2-1). Fifty percent of the area of the California small estuaries had
silver concentrations less than 0.11 ug/g and 90% of the area had concentrations less
than 0.51 ug/g (Figure 3.2-21). Silver was detected at all 26 Northern California river
stations. Silver averaged 0.05 ug/g in the Northern California rivers with a maximum
73
-------
concentration of 0.11 |jg/g in the Klamath River (Table 3.2-2). Fifty percent of the area
of the Northern California rivers had silver concentrations less than 0.04 |jg/g and 90%
of the area had concentrations less than 0.08 |jg/g (Figure 3.2-22). Silver
concentrations exceeded the ERL only at 1 California small estuary station (0.3% of
area) (Tables 3.2-1, 3.2-2).
Tin
Tin was detected at all 47 California small estuary stations. Tin averaged 2.55 ug/g in
these stations with a maximum concentration of 17.3 ug/g in the Los Angeles Harbor
(Table 3.2-1). Fifty percent of the area of the California small estuaries had tin
concentrations less than 1.78 ug/g and 90% had concentrations less than 5.16 ug/g
(Figure 3.2-23). Tin was detected at all 26 Northern California river stations. Tin
averaged 1.45 in the Northern California rivers with a maximum of 11.6 in the Albion
River (Table 3.2-2). Fifty percent of the area of the Northern California rivers had tin
concentrations less than 1.06 ug/g and 90% of the area had concentrations less than
1.90 ug/g (Figure 3.2-24).
Zinc
Zinc was detected at all 47 California small estuary stations. Zinc averaged 73.1 ug/g in
these stations with a maximum concentration of 538 ug/g in the Los Angeles Harbor
(Table 3.2-1). No other station in the California small estuaries had a concentration
>175 ug/g. Fifty percent of the area of the California small estuaries had zinc
concentrations less than 51.6 ug/g and 90% of the area had concentrations less than
127.9 ug/g (Figure 3.2-25). Zinc was detected at all 26 Northern California river
stations. Zinc averaged 43.1 ug/g in the Northern California rivers with a maximum
concentration of 76.8 ug/g in the Smith River (Table 3.2-2). Fifty percent of the area of
the Northern California rivers had zinc concentrations less than 45.3 ug/g and 90% of
the area had concentrations less than 72.4 ug/g (Figure 3.2-25). Zinc concentrations
exceeded the ERL at 4 California small estuary stations (6% of area), and 1 station
(0.3% of area) had a value exceeding the ERM (Table 3.2-1). No Northern California
river stations exceeded either the ERL or ERM for zinc (Table 3.2-2).
Additional Metals
In addition to the 11 metals discussed above, aluminum, antimony, iron, and
manganese were measured in the sediments. The mean concentration and frequency
of detection for each of these metals in the California small estuaries are given in Table
3.2-1 and the corresponding values for the Northern California rivers are given in Table
3.2-2. Each of these four metals was detected at all of the stations in both the California
small estuaries and the Northern California rivers. Not unexpectedly, aluminum and
iron were the two most abundant metals, with mean concentrations ranging from about
24,000 ug/g to 40,000 ug/g.
74
-------
Table 3.2-1 Summary statistics for sediment metal concentrations (ug/g, dry weight) for the California small estuary
stations (N=47). The mean and standard deviation (SD) were calculated using all the data, including the non-detects
which were set to 0. The "mean when present" was calculated using the samples which had detectable concentrations of
the compound. ERL and ERM values are from Long et al. (1995).
Metal
Aluminum
Antimony
Arsenic
Cadmium
Chromium
Copper
Iron
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Tin
Zinc
Overall
Mean
Concen-
tration
39,677
1.10
7.38
0.36
143.3
35.12
26,562
25.90
359.6
0.172
32.07
0.280
0.195
2.55
73.11
Overall
SD
1 1 ,552
2.35
3.50
0.62
191.7
61.43
1 1 ,420
43.15
160.79
0.353
28.34
0.319
0.230
2.73
82.76
Mean
Concen-
tration
when
Present
39,677
1.10
7.38
0.36
143.3
35.12
26,562
25.90
359.6
0.208
32.07
0.306
0.195
2.55
73.11
Min
9420
0.05
1.74
0.04
11.7
2.48
7160
4.23
106
0
3.34
0
0.03
0.557
7.89
Max Frequency ERL
of
detection
69,200
16.40
17.10
4.30
927
398.0
49,400
293
769
2.33
116
0.177
1.13
17.3
538
47
47
47
47
47
47
47
47
47
39
47
43
47
47
47
8.2
1.2
81
34
46.7
0.15
20.9*
2.0
1.0
150
ERM
70.0
9.6
370
270
218
0.71
51.6*
25.0
3.7
410
>ERL
No.
Sites
18
1
21
15
5
15
23*
0
1
4
>ERM
No.
Sites
0
0
4
1
1
1
8*
0
0
1
>ERL
%
Area
46
0.1
58
32
8
42
54*
0
0.3
6
>ERM
%
Area
0
0
9
0.3
0.3
0.3
22*
0
0
0.3
-J
Ol
' The ERL and ERM for nickel has low reliability for the West Coast. See text for discussion.
-------
Table 3.2 -2. Summary statistics for sediment metal concentrations (ug/g, dry weight) for the Northern California river
stations (N=26). The mean and the standard deviation (SD) were calculated using all the data, including the non-detects
which were set to 0. The "mean when present" was calculated using the samples which had detectable concentrations of
the compound. ERL and ERM values are from Long et al. (1995).
Metal
Aluminum
Antimony
Arsenic
Cadmium
Chromium
Copper
Iron
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Tin
Zinc
Overall
Mean
Concen-
tration
24,356
0.552
6.92
0.081
316.9
17.75
30,023
9.35
396.7
0.232
93.75
0.124
0.048
1.45
43.07
Overall
SD
10,010
0.287
1.64
0.050
438.7
11.89
10,442
6.04
191.4
0.646
104.48
0.110
0.024
2.12
18.29
Mean
Concen-
tration
when
Present
24,356
0.552
6.92
0.081
316.9
17.75
30,023
9.35
396.7
0.241
93.75
0.147
0.048
1.45
43.07
Min
3030
0.229
3.97
0.025
9.19
2.66
1 1 ,200
2.99
108
0
4.65
0
0.02
0.175
11.4
Max Frequency ERL
of
detection
40,600
1.58
10.80
0.206
1770
43.6
48,600
33.5
733
3.11
354
0.394
0.11
11.6
76.8
26
26
26
26
26
26
26
26
26
25
26
22
26
26
26
8.2
1.2
81
34
46.7
0.15
20.9*
2.0
1.0
150
ERM
70.0
9.6
370
270
218
0.71
51.6*
25.0
3.7
410
>ERL
No.
Sites
7
0
16
5
0
2
18*
0
0
0
>ERM
No.
Sites
0
0
6
0
0
2
12*
0
0
0
>ERL
%
Area
22
0
80
23
0
20
81*
0
0
0
>ERM
%
Area
0
0
34
0
0
9
68*
0
0
0
-J
CD
' The ERL and ERM for nickel has low reliability for the West Coast. See text for discussion.
-------
Sediment Arsenic Concentration
California Small Estuaries
100 -
60 -
40 -
20 -
6 8 10 12 14
Concentration (ug/g)
16 18
Figure 3.2 -5. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of arsenic.
Sediment Arsenic Concentration
Northern California Rivers
100 -
< 80
'c
01
u
S. 60
O
20 -
-Cumulative Percent
• 95% Confidence Interv;
4 6 £
Concentration (ug/g)
10
12
Figure 3.2 -6. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of arsenic.
77
-------
100 -
80 -
« 60-|
m
E
3
O
40 -
20 -
Sediment Cadmium Concentration
California Small Estuaries
Cumulative Percent
- - 95% Confidence Interval
2 3
Concentration (ug/g)
Figure 3.2 -7. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of cadmium.
Sediment Cadmium Concentration
Northern California Rivers
100 -
< 80 -
£ 60-1
0)
*PB
5 40-1
O
20 -
0.05 0.1 0.15
Concentration (ug/g)
0.2
0.25
Figure 3.2 -8. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of cadmium.
78
-------
Sediment Chromium Concentration
California Small Estuaries
100 -
40 -
Cumulative Percent
- - - - 95% Confidence Interval
400 600 800
Concentration (ug/g)
Figure 3.2 -9. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of chromium.
Sediment Chromium Concentration
Northern California Rivers
100 -
< 80
01
JS
3
3
o
60 -I
40 -
20 -
Cumulative Percent
. . . . 95% Confidence Interval
0 200 400 600 800 1000 1200 1400 1600 1800 2000
Concentration (ug/g)
Figure 3.2 -10. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of chromium.
79
-------
Sediment Copper Concentration
California Small Estuaries
100 -
80 -
60 -
-Cumulative Percent
- - - - 95% Confidence Interval
0 50 100 150 200 250 300 350 400 450
Concentration (ug/g)
Figure 3.2-11. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of copper.
Sediment Copper Concentration
Northern California Rivers
100 -
0. 60
ro
5 40
O
20 -
10 20 30
Concentration (ug/g)
40
50
Figure 3.2 -12. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of copper.
80
-------
100 -
S 80 -
40 -
Sediment Lead Concentration
California Small Estuaries
-Cumulative Percent
. - . - 95% Confidence Interval
100 150 200 250
Concentration (ug/g)
Figure 3.2 -13. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of lead.
Sediment Lead Concentration
Northern California Rivers
100 -
01
Q_
5 40 -
20 -
10 15 20 25
Concentration (ug/g)
30
35
40
Figure 3.2 -14. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of lead.
81
-------
Sediment Mercury Concentration
California Small Estuaries
100 -
E
3
o
60 -
40 -
20 -
0.5
Cumulative Percent
... -95% Confidence Interval
1 1.5
Concentration (ug/g)
2.5
Figure 3.2 -15. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of mercury.
Sediment Mercury Concentration
Northern California Rivers
0.5
1 1.5 2 2.5
Concentration (ug/g)
3.5
Figure 3.2 -16. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of mercury.
82
-------
Sediment Nickel Concentration
California Small Estuaries
100 -
Si
01 60
Q_
40 60 80 100
Concentration (ug/g)
Figure 3.2 -17. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of nickel.
Sediment Nickel Concentration
Northern California Rivers
100 -
60 -I
3
O
40 -
20 -
0 50 100 150 200 250 300 350
Concentration (ug/g)
400
Figure 3.2 -18. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of nickel.
83
-------
Sediment Selenium Concentration
California Small Estuaries
100 -
80 -
£ 60
•s
"5 40
|
o
20 -
0.2 0.4 0.6 0.8 1 1.2
Concentration (mg/kg)
1.4
Figure 3.2-19. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of selenium.
Sediment Selenium Concentration
Northern California Rivers
100 -
80 -
60 -
•5 40 -
O
20 -
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45
Concentration (mg/kg)
Figure 3.2-20. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of selenium.
84
-------
Sediment Silver Concentration
California Small Estuaries
100 -
<
•E
HI
Q.
HI
80 -
60 -
•5 40 -
O
20 -
0.2 0.4 0.6 0.8
Concentration (mg/kg)
1.2
Figure 3.2 -21. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of silver.
Sediment Silver Concentration
Northern California Rivers
100 -
80 -
£ 60
3 40
O
20 -
0.02 0.04 0.06 0.08 0.1
Concentration (mg/kg)
0.12
Figure 3.2 -22. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of silver.
85
-------
Sediment Tin Concentration
California Small Estuaries
100 -
<
•E
u
Q.
HI
80 -
60 -
3 40-
20 -
-Cumulative Percent
• 95% Confidence Interval
8 10 12 14
Concentration (mg/kg)
16 18 20
Figure 3.2 -23. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of tin.
Sediment Tin Concentration
Northern California Rivers
100 -
80 -
s. 60
•5 40 -
O
20 -
-Cumulative Percent
• 95% Confidence Interval
468
Concentration (mg/kg)
10
12
Figure 3.2 -24. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of tin.
86
-------
Sediment Zinc Concentration
California Small Estuaries
100 -
80 -
60 -
•5 40 -
o
20 -
-Cumulative Percent
- 95% Confidence Interval
100 200 300 400
Concentration (mg/kg)
500
600
Figure 3.2 -25. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of zinc.
Sediment Zinc Concentration
Northern California Rivers
100 -
HI
o
Q.
HI
>
E
o
80 -
60 -
40 -
20 -
t-J
rm-'
10 20 30 40 50 60 70 80
Concentration (mg/kg)
90
Figure 3.2 -26. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of zinc.
87
-------
3.2.2.2 Sediment Organics
Sediment Organics
Concentrations of sediment organic pollutants were measured at 47 stations in the
California small estuaries and in 26 stations in the Northern California rivers. The mean
concentration of each organic compound was calculated with the non-detects (i.e., less
than the MDL) set to 0 (see Table 2.8 for the MDLs). For comparative purposes, mean
concentrations of the organic compounds were also calculated using the subset of
samples in which the compounds were detected.
Total PAHs
PAHs were detected at 36 of the 47 California small estuary stations. Total PAHs
averaged 685 ug/kg in the California small estuary stations with a maximum
concentration of 22,982 ug/kg in the Los Angeles Harbor (Table 3.2 - 3). The
compounds 2,6-Dimethylnaphthalene, 2,3,5-Trimethylnaphthalene, and 1-
Methylphenanthrene constituted 61 % of the total PAHs at the Los Angeles Harbor site.
Eighteen percent of area of California small estuaries had undetectable concentrations
of PAHs. Fifty percent of the area of the California small estuaries had total PAH
concentrations less than 53 ng/g and 90% of the area had concentrations less than 422
ng/g (Figure 3.2-27). The ERL was exceeded at two stations for high molecular weight
PAHs, and one station each for low molecular weight and total PAHs. The ERM was
exceeded only at one station for low molecular weight PAHs (Table 3.2 - 3).
PAHs were detected at 11 of the 26 Northern California river stations. Total PAHs
averaged 155 ng/g in the Northern California river stations with a maximum
concentration of 2653 ng/g in the Albion River (Table 3.2 - 4). Sixty-one percent of the
area of the Northern California rivers had undetectable concentrations of PAHs while
90% of the area had concentrations less than 234 ng/g (Figure 3.2-28). On the
average, low molecular weight PAHs constituted 69% of the total PAHs and high
molecular weight PAHs constituted 31% of the total PAHs in the California small
estuaries. In comparison, the high molecular weight PAHs constituted a relatively
greater percentage of the total PAHs in the Northern California rivers, making up 66% of
the total PAHs while the low molecular weight PAHs constituted 34% of the total PAHs.
The ERL was exceeded only at one station for high molecular weight PAHs, and the
ERM was not exceeded at any station (Table 3.2 - 4).
Total PCBs
PCBs were detected at 13 of the 47 California small estuary stations. Total PCBs
averaged 5.85 ng/g in the California small estuary stations with maximum
concentrations of 90.3 ng/g in San Diego Bay and 69.1 ng/g in the Los Angeles Harbor
(Table 3.2 - 3). Seventy percent of the area of the California small estuaries had
undetectable concentrations of PCBs while 90% of the area had concentrations less
than 12.3 ng/g (Figure 3.2-29). The ERL was exceeded at three stations (5.8% of
area), while the ERM was not exceeded at any station (Table 3.2 - 3).
88
-------
PCBs were detected at 8 of the 26 (31%) Northern California river stations. Total PCBs
averaged 2.72 ng/g in the Northern California river stations with a maximum of 22.7
ng/g in the Albion River (Table 3.2 - 4). Eighty-four percent of the area of the Northern
California rivers had undetectable levels of PCBs while 90% of the area had
concentrations less than 1.34 ng/g (Figure 3.2-30). Averaged across all the California
stations (N=73), PCB110, PCB138, and PCB153 were the most frequently detected
congeners while PCBS, PCB138, and PCB195 had the highest mean concentrations.
The ERL was exceeded at one station (3.2% of area), while the ERM was not exceeded
at any station (Table 3.2 - 4).
Total DDT
DDT or one of its metabolites was detected at 16 of the 47 of the California small
estuary stations. Total DDT averaged 12.96 ng/g in the California small estuaries with a
maximum concentration of 301.2 ng/g in the Channel Island Harbor in Southern
California (Table 3.2 - 3). The only two other values >50 ng/g were the 99 and 50
ng/g concentrations in the Long Beach Harbor and the Los Angeles Harbor,
respectively. 4,4'-DDE was the most frequently detected DDT compound and had the
highest mean concentration in the California small estuaries. Seventy-four percent of the
area of the California small estuaries had undetectable levels of DDT and its metabolites
while 90% of the area had concentrations less than 22.29 ng/g (Figure 3.2-31). The
ERLs for both total DDT and 4,4'-DDE were exceeded at 14 stations (22% of area), and
the ERMs were both exceeded at 3 stations (5.8% of area). DDT and its metabolites
were not detected at any of the Northern California river stations (Table 3.2 - 4).
Additional Pesticides
Besides DDT, an additional 12 pesticides were measured in the sediments in the California
small estuaries (Table 3.2 - 3) and in the Northern California rivers (Table 3.2 - 4). Of these
Aldrin, Dieldrin, Endosulfan I, Endosulfan II, Endosulfan Sulfate, Heptachlor, Heptachlor
Epoxide, Lindane (gamma-BHC) and Mirex were never detected at any of the stations. Of
the remaining three pesticides, Endrin had the highest average concentration in both the
California small estuaries and in the Northern California rivers. At all 9 stations where
Endrin was detected, the value exceeded the ERL but not the ERM (Tables 3.2-3, 3.2.4).
Trans-nonachlor was the second most abundant of these additional pesticides in both the
California small estuaries and the Northern California rivers. There were an insufficient
number of detects to calculate CDFs for any of the additional pesticides.
89
-------
Table 3.2-3. Summary statistics for sediment organic pollutants (ng/g, dry weight) for the California small estuary stations (N=47). The
mean and standard deviation (SD) were calculated using all the data, including the non-detects which were set to 0. The "mean when
present" was calculated using the samples which had detectable concentrations of the compound. ERL and ERM values are from Long
et al. (1995). NA - not analyzed, see text.
Analyte Overall mean Overall Mean
concentration SD concentration
ng/g dry wt when
present
HMW PAHs
LMW PAHs
Total PAHs
Total PCBs
2,4'-DDD
2,4'-DDE
2,4'-DDT
4,4'-DDD
4,4'-DDE
4,4'-DDT
Total DDT
Aldrin
Alpha-chlordane
Dieldrin
Endosulfan I
Endosulfan II
Endosulfan
Sulfate
Endrin
Heptachlor
Heptachlor
Epoxide
Lindane
(gamma-BHC)
Mi rex
Trans-nonachlor
471.96
213.21
685.17
5.85
0.349
0.740
0.768
1.06
9.99
0.059
12.96
0
0.270
0
0
0
0
0.479
0
0
0
0
0.310
2921.95
572.46
3356.15
17.09
1.57
2.35
NA
4.18
34.84
NA
46.39
0
0.83
0
0
0
0
1.85
0
0
0
0
1.38
1109.10
313.16
894.53
21.13
5.47
4.97
36.1
7.10
29.35
2.8
38.08
0
2.54
0
0
0
0
7.50
0
0
0
0
3.64
Min
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Max Frequency ERL ERM >ERL
of
detection No. Sites
20,064
2918
22,982
90.3
9.2
13.6
36.1
26.7
224
2.8
301.2
0
3.5
0
0
0
0
7.50
0
0
0
0
8.6
20 1700 9600 2
32 552 3160 1
36 4022 44792 1
13 22.7 180 3
3
7
1
7
16 2.2 27.0 14
1
16 1.58 46.1 14
0
5
0 0.02 8 0
0
0
0
3 0.02 45 3
0
0
0
0
4
>ERM >ERL >ERM
No. Sites Area % Area %
0 0.3 0
1 0.3 0.3
0 0.3 0
0 5.8 0
3 21.7 5.8
3 21.7 5.8
0 NA NA
0 NA NA
CD
O
-------
Table 3.2-4. Summary statistics for sediment organic pollutants (ng/g, dry weight) for the Northern California river stations (N=26). The
mean and standard deviation (SD) were calculated using all the data, including the non-detects which were set to 0. The "mean when
present" was calculated using the samples which had detectable concentrations of the compound. ERL and ERM values are from Long
et al. (1995). NA - not analyzed, see text.
Analyte Overall mean Overall Mean Min
concentration SD concentration
ng/g dry wt when
present
HMW PAHs
LMW PAHs
Total PAHs
Total PCBs
2,4'-DDD
2,4'-DDE
2,4'-DDT
4,4'-DDD
4,4'-DDE
4,4'-DDT
Total DDT
Aldrin
Alpha-chlordane
Dieldrin
Endosulfan I
Endosulfan II
Endosulfan
Sulfate
Endrin
Heptachlor
Heptachlor
Epoxide
Lindane
(gamma-BHC)
Mi rex
Trans-nonachlor
52.04
102.96
155.00
2.72
0
0
0
0
0
0
0
0
0
0
0
0
0
1.73
0
0
0
0
0.974
112.75
463.24
524.97
5.73
0
0
0
0
0
0
0
0
0
0
0
0
0
3.22
0
0
0
0
2.94
135.30
267.70
366.36
8.84
0
0
0
0
0
0
0
0
0
0
0
0
0
7.50
0
0
0
0
8.44
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Max Frequency ERL ERM >ERL
of
detection No. Sites
427
2370
2653
22.7
0
0
0
0
0
0
0
0
0
0
0
0
0
7.50
0
0
0
0
12.7
10 1700 9600 1
10 552 3160 0
11 4022 44792 0
8 22.7 180 1
0
0
0
0
0 2.2 27.0 0
0
0 1.58 46.1 0
0
0
0 0.02 8 0
0
0
0
6 0.02 45 6
0
0
0
0
3
>ERM >ERL >ERM
No. Sites Area % Area %
0 3.1 0
000
000
0 3.2 0
000
000
0 NA NA
0 NA NA
CD
-------
Sediment Total PAH Concentration
California Small Estuaries
S. 60
20 -
-Cumulative Percent
-95% Confidence Interval
5000 10000 15000
Concentration (ug/kg dry)
20000
25000
Figure 3.2 -27. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of total PAH's.
Sediment Total PAH Concentration
Northern California Rivers
100 -
< 80
S. 60
40-|
O
20 -
-
. . . -95% Confidence Interval
500 1000 1500 2000
Concentration (ng/g dry)
2500
3000
Figure 3.2 -28. Percent area (and 95% C.I.) of Northern California rivers vs. sediment
concentration of total PAH's.
92
-------
Sediment Total PCB Concentration
California Small Estuaries
100 -
u
o
HI
Q.
"5 40 -
E
o
20 -
-Cumulative Percent
- 95% Confidence Interval
10 20 30 40 50 60 70
Concentration (ug/kg dry)
90 100
Figure 3.2 -29. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of total PCB.
Sediment Total PCB Concentration
Northern California Rivers
100 -
re
v
< 80
'c
-------
Sediment DDT Concentration
California Small Estuaries
100 -
80 -
I eo ^
"5 40 -
|
O
20 -
-Cumulative Percent
- 95% Confidence Interval
50 100 150 200 250
Concentration (ug/kg dry)
300
350
Figure 3.2 -31. Percent area (and 95% C.I.) of California small estuaries vs. sediment
concentration of total DDT.
94
-------
3.2.3 Sediment Toxicity
3.2.3.1 Ampelisca abdita
Sediment for toxicity tests with the amphipod Ampelisca abdita was successfully
collected at 47 of the 50 California small estuaries stations, and 26 of the 30 Northern
California rivers stations (see section 2.6). Control conditions for a successful toxicity
test with this species require a mean of 90% survival in the five replicates in control
sediments, with no replicate less than 80%. These requirements were not met in 11 of
the 47 California small estuaries samples, and these were excluded from the CDF
analysis, leaving 36 successful toxicity tests of the 50 California small estuaries
stations, and 26 of the 30 Northern California rivers stations.
The control corrected mean survivorship of A. abdita was < 80% in sediment toxicity
tests in approximately 1 % of the area of the small estuaries (Figure 3.2 -32) and 39% of
the area of the Northern California rivers (Figure 3.2 -33). One station in the Los
Angeles River had control corrected mean survivorship equal to zero. Two of the sites
in the northern California rivers, both in the Smith River, had control corrected mean
survivorship less than 50%. Control corrected mean survivorship > 100%, indicates
better survival of amphipods in test sediments than in controls.
3.2.3.2 Eohaustorius estuarius
Sediment toxicity tests with the amphipod Eohaustorius estuarius were conducted on
the same sediments as the tests with A. abdita. Control conditions for a successful
toxicity test with E. estuarius require a mean of 90% survival in the five replicates in
control sediments, with no replicate less than 80%. These requirements were met in
all of the 62 California small estuaries and Northern California rivers samples tested
with E. estuarius.
The control corrected mean survivorship of E estuarius in sediment toxicity tests was
< 80% in approximately 18.8% of the area of the California small estuaries and 24.1% of
the area of the Northern California rivers. Two stations, in the San Diego River and the
Los Angeles River, had control corrected mean survivorship less than 50%.
3.2.3.3 Arbacia punctulata
Sediment porewater toxicity tests with sea urchins, Arbacia punctulata were conducted
on 47 California small estuary stations in California. No sediments from the 30 Northern
California rivers were tested with A. punctulata. For consistency in analysis, the results
of the two sets of A. punctulata porewater toxicity tests are each presented as CDF's for
each of the three dilution treatments.
95
-------
In the egg fertilization test, toxicity to A. punctulata (expressed as fertilization success
significantly different from control) was observed in 21.5, 6.7 and 5.8 % of the area of
the small estuaries for the 100, 50 and 25% dilutions (Figs 3.2-36, 3.2-37 and 3.2-38).
In the embryological development test, toxicity (expressed as embryological
development success significantly different from control) was observed in approximately
95, 57.4 and 2.7 % of the area of the small estuaries for the 100, 50 and 25% dilutions
(Figs 3.2-39, 3.2-40 and 3.2-41).
96
-------
Percent Survival of Ampelisca abdita
California Small Estuaries
100 -
ro
S!
< 80
'c
Ol
5 60 H
2 40 H
o
20 -
-Cumulative Percent
-95% Confidence Interval
20 40 60 80 100
Percent Control Corrected Survival (%)
120
Figure 3.2 - 32. Percent area (and 95% C.I.) of California small estuaries vs. percent
control corrected survivorship of Ampelisca abdita.
Percent Survival of Ampelisca abdita
Northern California Rivers
100 -
ro
S!
< 80
'c
Ol
5 60 H
2 40 H
o
20 -
0 20 40 60 80 100
Percent Control Corrected Survival (%)
120
Figure 3.2 - 33. Percent area (and 95% C.I.) of Northern California rivers vs. percent
control corrected survivorship of Ampelisca abdita.
97
-------
Percent Survival of Eohaustorius estuarius
California Small Estuaries
100 -
ro
a;
S. 60
Ol
3
=
o
40 -
20 -
-Cumulative Percent
- 95% Confidence Interval
20 40 60 80 100
Percent Control Corrected Survival (%)
120
Figure 3.2 - 34. Percent area (and 95% C.I.) of California small estuaries vs. percent
control corrected survivorship of Eohaustorius estuarius.
Percent Survival of Eohaustorius estuarius
Northern California Rivers
100 -
80 ]
£ 60 ]
I
H 40 -
3
° 20 -
-Cumulative Percent
- 95% Confidence Interval
0 20 40 60 80 100
Percent Control Corrected Survival (%)
120
Figure 3.2 - 35. Percent area (and 95% C.I.) of Northern California rivers vs. percent
control corrected survivorship of Eohaustorius estuarius.
98
-------
Percent Egg Fertilization Success
of Arbacia punctulata - 100% of
Water Quality Adjusted Porewater
California Small Estuaries
100 -
HI
Q.
60 -
_re 40 -
3
E
" 20 -I
-Cumulative Percent
- 95% Confidence Interval
20 40 60 80 100
Percent Egg Fertilization Success (%)
120
Figure 3.2 - 36. Percent area (and 95% C.I.) of California small estuaries vs. percent
fertilization success of Arbacia punctulata eggs for the 100% water quality
adjusted porewater concentration.
Percent Egg Fertilization Success
of Arbacia punctulata - 50% of
Water Quality Adjusted Porewater
California Small Estuaries
100 -
c
HI
u
HI
Q.
™
3
E
3
o
80 -
60 -
40 -
-Cumulative Percent
-95% Confidence Interval
20 40 60 80 100
Percent Egg Fertilization Success (%)
120
Figure 3.2 - 37. Percent area (and 95% C.I.) of California small estuaries vs. percent
fertilization success of Arbacia punctulata eggs for the 50% water quality
adjusted porewater concentration.
99
-------
Percent Egg Fertilization Success
of Arbacia punctulata - 25% of
Water Quality Adjusted Porewater
California Small Estuaries
100 -
< 80
60 -
40 -
20 -
-Cumulative Percent
-95% Confidence Interval
20 40 60 80 100
Percent Egg Fertilization Success (%)
120
Figure 3.2 - 38. Percent area (and 95% C.I.) of California small estuaries vs. percent
fertilization success of Arbacia punctulata eggs for the 25% water quality
adjusted porewater concentration.
Percent Embryonic Development Success
of Arbacia punctulata -100% of
Water Quality Adjusted Porewater
California Small Estuaries
-Cumulative Percent
-95% Confidence Interval
20 40 60 80 100
Percent Embryonic Development Success (%)
120
Figure 3.2 - 39. Percent area (and 95% C.I.) of California small estuaries vs. percent
embryonic development success of Arbacia punctulata for the 100% water
quality adjusted porewater concentration.
100
-------
Percent Embryonic Development Success
of Arbacia punctulata - 50% of
Water Quality Adjusted Pore water
California Small Estuaries
100 -
HI
Q.
HI
60 -
a 40 -
3
3
0 20 -
.
r^ i i- n j.
. . . -95% Confidence Interval
20 40 60 80 100
Percent Embryonic Development Success (%)
120
Figure 3.2 - 40. Percent area (and 95% C.I.) of California small estuaries vs. percent
embryonic development success of Arbacia punctulata for the 50% water quality
adjusted porewater concentration.
Percent Embryonic Development Success
of Arbacia punctulata - 25% of
Water Quality Adjusted Porewater
California Small Estuaries
100 -
re
Si
£. 60-
]3 40 -
3
|
O 20 -
-Cumulative Percent
- 95% Confidence Interval
20 40 60 80 100
Percent Embryonic Development Success (%)
120
Figure 3.2 - 41. Percent area (and 95% C.I.) of California small estuaries vs. percent
embryonic development success of Arbacia punctulata for the 25% water quality
adjusted porewater concentration.
101
-------
3.2.4 Tissue Contaminants
Residues of a suite of metals, PCBs, and pesticides were measured in the whole bodies
offish at 33 stations in the California small estuaries and 14 stations in the Northern
California rivers (see Table 2-5 for list of compounds). Residues were not measured at
the other stations because of the unavailability of fish at the sites or the inability to
sample because of shallow water or other difficulties. Flatfish (pleuronectiformes) were
the designated target species while various perch-like species (perciformes) were the
secondary target group when flatfish were not captured. If neither flatfish nor perciform
species were present, whatever abundant species was captured at the site was utilized
as an "other" group. The specific fish species in each group and their relative
abundances are given in Tables 3.2-5 and 3.2-6. Because of difficulty of capturing the
target species, 12 of the 14 sites with residues measured in the "other" species
occurred in the Northern California rivers compared to only two sites in the California
small estuaries. Combining all fish groups, residues were measured in 54 samples from
33 sites in the California small estuaries, and in 19 samples from 14 sites in the
Northern California rivers (Tables 3.2-7 through 3.2-10). Of these sites, residues were
measured in the target flatfish at 24 small estuary and 3 Northern California river sites.
Because it is not clear that the sites without any fish captured for residue analysis were
distributed randomly, and because of the uncertainties associated with mixing different
guilds offish species with different lipid content, the fish residue data are presented as
summary statistics rather than CDFs to estimate areas.
Fish tissue residues of the 12 metals are summarized in Tables 3.2-7 and 3.2-8 for all fish
species combined and for each fish group in the California small estuaries and the
Northern California rivers, respectively. Aluminum, with an average concentration of 96.4
ug/g (wet weight) for all fish species in the small estuaries and 166 ug/g in the northern
rivers, had a residue about two- to fifteen-times greater than zinc, the metal with the
second highest concentration. Silver, mercury, cadmium, and lead had the lowest
residues with all four having a mean concentration <0.1 ug/g when averaged for all
species. Concentrations of the various metals were generally similar among the three
fish groups within the small estuaries and within the northern rivers. The greatest relative
difference was for nickel, which displayed a 10-fold range among fish groups in both the
small estuaries and Northern California rivers. The pattern of metal residues as well as
the absolute concentrations were also relatively similar between the small estuaries and
the Northern California rivers. When all fish groups were combined, the greatest
difference was for nickel which about 8-fold greater in the Northern California rivers
compared to the overall average for the small estuaries (2.15 ug/g versus 0.26 ug/g).
Though the mean values were similar, the location of the maximum tissue residues
varied for each of the metals. The highest concentrations of aluminum, chromium and
nickel were in samples from the Big River and the highest concentration of manganese
was in the Klamath River, both within the Northern California rivers. In comparison, the
highest concentrations of zinc and silver were in Big Lagoon, the highest selenium and
lead values were in Long Beach Harbor, and the highest copper value occurred in San
102
-------
Diego Bay. The highest arsenic value was in Humboldt Bay. The highest values for
mercury occurred in San Diego Bay and the Albion River.
Fish tissue residues of total PCBs, total DDT, and other pesticides are summarized in
Tables 3.2 -7 and 3.2-8. Total DDT had the highest residue of all the neutral organic
contaminants, averaging 153 ng/g over all fish species in samples from the California
small estuaries and 1.03 ng/g in the Northern California rivers. In all three fish groups
4,4'-DDE constituted 95% to 100% of the total DDT. In contrast to the metals, total DDT
showed a considerable difference among the fish groups, with average values ranging
from 1.27 ng/g in the other group, 32.6 ng/g in the flatfish, to 244 ng/g in the perciform
species.
Total PCBs had the second highest residue of the neutral organics, averaging 43.7 ng/g
for all fish species in the California small estuaries and 1.53 ng/g in the Northern California
rivers. PCB138 and PCB153 were the two most abundant PCB congeners, their sum
averaging 35% of the total PCBs in the three fish groups overall. As with total DDT, total
PCBs showed a considerable difference among the fish groups, ranging from undetected
in the "other" group to 96.9 ng/g in the perciform species in the California small estuaries.
It is possible that these differences in DDT and PCB residues among fish groups are to a
large extent a result of where the different types of fish species were collected rather than
an inherent difference in bioaccumulation by the fish groups. Genyonemus lineatus (white
croaker) was the most abundant species in the perciform group, and all the white croaker
used for fish residues were obtained from either the Los Angeles Harbor or the Long
Beach Harbor. These two industrialized harbors were the sites for the maximum fish
residues for both total PCBs and total DDT as well as having relatively high sediment
concentrations of total PCB and total DDT. In comparison, most of the individuals making
up the "other" group were captured in the non-industrialized small Northern California
estuaries. In addition to the effects of collecting site, the higher lipid content in the
perciform fish may also have contributed to the differences in residues among fish groups,
as discussed below.
The residues of the thirteen additional pesticides were considerably lower than that of total
PCBs and total DDT (Table 3.2 -5). Tissue analysis failed to detect measurable
concentrations of any of the following compounds in samples from either California small
estuaries or the Northern California rivers: Aldrin, Dieldrin, Endosulfan I and II, Endosulfan
sulfate, Endrin, Heptachlor, Heptachlor epoxide, Lindane, Mirex and Toxaphene. Alpha-
chlordane, Gamma-chlordane and Trans-nonachlor were not detected in the Northern
California rivers. Of the three pesticides that were detected in the California small
estuaries, Trans-nonachlor had the highest residue with a concentration of 1.68 ng/g wet
weight when averaged over all the fish species, while Gamma-chlordane averaged 1.09
ng/g and Alpha-chlordane averaged 0.57 ng/g. The three fish groups showed differences
in the mean residues of these pesticides with higher residues of all three pesticides in the
perch-like species. As mentioned above, differences in where the various species groups
were collected may have contributed to these among-group differences in residue
patterns.
103
-------
Bioaccumulation of neutral organic pollutants, such as PCB and DDT, often increases at
higher lipid content. Tissue lipid content measured in the three groups offish from
California small estuaries and Northern California rivers indicated significant differences
between the flatfish and the perciform groups, but no difference between either of those
groups and the "other" fish group (Table 3.2-11). Statistical analysis was based on one-
way ANOVA with Tukey test on log transformed data. The data were transformed to meet
the assumptions of normality and equal variance. The approximate 2-fold greater lipid
content in the perciform group compared to the flatfish may have contributed to the
higher Total DDT and Total PCB residues in the California small estuaries.
104
-------
Table 3.2 -5. The species composition and relative abundances of the three fish groups
used in the tissue residue analysis from California small estuaries. "Number" indicates
the number of samples analyzed for residues, which may consist of a composite of
more than one individual depending upon the size of the fish. The percent within a
group is the relative abundance of the species within the group in which it is included
based on the number of samples. The overall percent is the relative abundance of the
species when all the fish species are combined. Total number of samples = 54.
Fish Group
Pleuronectiformes
Citharichthys stigmaeus
Pleuronectes vetulus
Paralichthys californicus
Citharichthys sordidus
Symphurus atricauda
Perciformes
Genyonemus lineatus
Cymatogaster aggregate
Paralabrax nebulifer
Gasterosteus aculeatus
Paralabrax maculatofasciatus
Other
Atherinops affinis
Leptocottus armatus
Number
14
11
10
1
1
6
4
3
1
1
1
1
Percent within
Group
37.84
29.73
27.03
2.70
2.70
40.00
26.67
20.00
6.67
6.67
50.00
50.00
Overall Percent
25.93
20.37
18.52
1.85
1.85
11.11
7.41
5.56
1.85
1.85
1.85
1.85
Table 3.2 -6. The species composition and relative abundance of the three fish groups
used in the tissue residue analysis from Northern California rivers. "Number" indicates
the number of samples analyzed for residues, which may consist of a composite of
more than one individual depending upon the size of the fish. The percent within a
group is the relative abundance of the species within the group in which it is included
based on the number of samples. The overall percent is the relative abundance of the
species when all the fish species are combined. Total number of samples = 19.
Fish Group
Pleuronectiformes
Citharichthys stigmaeus
Pleuronectes vetulus
Paralichthys californicus
Perciformes
Genyonemus lineatus
Cymatogaster aggregate
Other
Atherinops affinis
Leptocottus armatus
Number
2
2
1
1
1
10
2
Percent within
Group
40.00
40.00
20.00
50.00
50.00
83.33
16.67
Overall Percent
10.53
10.53
5.26
5.26
5.26
52.63
10.53
105
-------
Table 3.2-7. Fish tissue residues of metals (ug/g wet weight) in California small
estuaries. Values for each fish group are the averages of all samples at a station, with
the samples consisting of individuals or composites of several individuals. The "All Fish"
group is the overall average combining all species. "Frequency of Detects" is the
number of stations where the metal was detected at a level above the minimum
detection limit (MDL). "No. Stations" is the number of stations in which a particular fish
group was analyzed. A total of 54 fish samples were analyzed at 33 stations in the
small estuaries.
Metal
All Fish
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
Pleuronectiformes
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
Perciformes
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
Mean
(ug/g wet)
96.40
0.85
0.04
1.05
0.88
0.08
4.28
0.04
0.26
0.48
0.01
12.58
72.70
0.83
0.06
2.11
0.59
0.04
4.26
0.03
0.28
0.41
0.00
10.95
125.93
0.85
0.02
0.30
1.27
0.12
4.84
0.05
0.10
0.55
0.01
14.06
SD
72.45
0.40
0.07
3.16
0.46
0.08
2.35
0.02
0.45
0.13
0.01
5.79
69.23
0.47
0.08
7.53
0.16
0.03
2.83
0.02
0.46
0.09
0.00
1.65
83.04
0.27
0.02
0.17
0.89
0.11
3.30
0.02
0.15
0.15
0.01
7.41
Mean when
Present
96.40
0.85
0.04
1.05
0.88
0.08
4.28
0.04
0.37
0.48
0.01
12.58
72.70
0.83
0.06
2.11
0.59
0.04
4.26
0.03
0.49
0.41
0.00
10.95
125.93
0.85
0.02
0.30
1.27
0.12
4.84
0.05
0.14
0.55
0.01
14.06
Minimum
3.36
0.34
0.00
0.08
0.31
0.00
1.69
0.01
0.00
0.32
0.00
7.84
3.36
0.34
0.00
0.07
0.30
0.00
1.69
0.01
0.00
0.32
0.00
7.90
15.20
0.48
0.00
0.12
0.68
0.01
1.56
0.01
0.00
0.35
0.00
7.84
Maximum
266.00
2.02
0.31
18.33
2.47
0.37
10.70
0.09
2.07
0.83
0.02
37.00
251.00
2.02
0.31
36.50
0.93
0.09
11.60
0.09
2.07
0.57
0.01
13.80
266.00
1.27
0.07
0.73
4.44
0.37
13.50
0.11
0.53
0.83
0.04
37.00
Frequency
of Detects/
No. Stations
33/33
33/33
33/33
33/33
33/33
33/33
33/33
33/33
23/33
33/33
30/33
33/33
23/23
22/23
22/23
23/23
23/23
23/23
23/23
23/23
13/23
23/23
19/23
23/23
16/16
16/16
16/16
16/16
16/16
16/16
16/16
16/16
11/16
16/16
16/16
16/16
106
-------
"Other"
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
168.00
0.47
0.02
1.34
1.71
0.06
5.46
0.05
1.18
0.50
0.01
19.60
63.64
0.04
0.01
0.13
0.15
0.02
0.20
0.02
0.39
0.02
0.00
13.29
168.00
0.47
0.02
1.34
1.71
0.06
5.46
0.05
1.18
0.50
0.01
19.60
123.00
0.44
0.02
1.25
1.60
0.04
5.32
0.03
0.90
0.48
0.01
10.20
213.00
0.50
0.03
1.43
1.81
0.07
5.60
0.06
1.46
0.51
0.01
29.00
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
107
-------
Table 3.2-8. Fish tissue residues of metals (ug/g wet weight) in Northern California
rivers. Values for each fish group are the averages of all samples at a station, with
samples consisting of individuals or composites of several individuals. The "All Fish"
group is the overall average combining all species. "Frequency of Detects" is the
number of stations where the metal was detected at a level above the minimum
detection limit (MDL). "No. Stations" is the number of stations in which a particular fish
group was analyzed. A total of 19 fish samples were analyzed at 14 stations in the
Northern California rivers.
Metal
All Fish
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
Pleuronectiformes
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
Perciformes
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
Mean
(ug/g wet)
165.98
0.34
0.02
2.93
1.42
0.06
6.43
0.03
2.15
0.40
0.01
13.05
101.03
0.43
0.02
0.96
1.01
0.04
3.93
0.03
0.73
0.40
0.00
11.64
33.25
0.36
0.01
1.46
1.63
0.01
10.44
0.03
0.23
0.41
0.01
21.25
SD
135.91
0.09
0.01
5.15
0.47
0.05
4.21
0.02
3.97
0.07
0.00
4.32
54.53
0.13
0.01
0.69
0.36
0.03
1.22
0.01
0.53
0.03
0.00
2.83
10.25
0.09
0.00
1.70
0.59
0.00
11.26
0.03
0.14
0.02
0.00
8.41
Mean when
Present
165.98
0.34
0.02
2.93
1.42
0.06
6.43
0.03
2.15
0.40
0.01
13.05
101.03
0.43
0.02
0.96
1.01
0.04
3.93
0.03
0.73
0.40
0.00
11.64
33.25
0.36
0.01
1.46
1.63
0.01
10.44
0.03
0.23
0.41
0.01
21.25
Minimum
36.05
0.23
0.00
0.26
0.67
0.01
2.32
0.00
0.07
0.26
0.00
9.46
69.30
0.29
0.02
0.30
0.67
0.02
2.53
0.02
0.19
0.37
0.00
9.81
26.00
0.30
0.01
0.26
1.21
0.01
2.47
0.01
0.13
0.39
0.01
15.30
Maximum
485.00
0.54
0.04
19.80
2.39
0.17
18.40
0.10
15.10
0.56
0.01
27.20
164.00
0.54
0.04
1.68
1.39
0.07
4.78
0.04
1.24
0.43
0.01
14.90
40.50
0.43
0.02
2.66
2.04
0.02
18.40
0.05
0.33
0.42
0.01
27.20
Frequency of
Detects/ No.
Stations
14/14
14/14
14/14
14/14
14/14
14/14
14/14
13/14
14/14
14/14
14/14
14/14
3/3
3/3
3/3
3/3
3/3
3/3
3/3
3/3
3/3
3/3
3/3
3/3
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
2/2
108
-------
"other"
Aluminum
Arsenic
Cadmium
Chromium
Copper
Lead
Manganese
Mercury
Nickel
Selenium
Silver
Zinc
180.26
0.31
0.01
3.17
1.44
0.07
5.50
0.03
2.37
0.39
0.01
11.93
140.65
0.06
0.01
5.56
0.43
0.06
2.72
0.03
4.27
0.08
0.00
1.81
180.26
0.31
0.01
3.17
1.44
0.07
5.50
0.03
2.37
0.39
0.01
11.93
46.10
0.23
0.00
0.28
1.01
0.01
1.79
0.00
0.06
0.26
0.00
9.46
485.00
0.43
0.03
19.80
2.39
0.17
10.50
0.10
15.10
0.56
0.01
15.60
12/12
12/12
12/12
12/12
12/12
12/12
12/12
11/12
12/12
12/12
12/12
12/12
109
-------
Table 3.2-9. Fish tissue residues of total PCBs, total DDT, and additional pesticides
(ng/g wet weight) in California small estuaries. Values for each fish group are the
averages of all samples at a station, with samples consisting of individuals or
composites of several individuals. The "All Fish" group is the overall average combining
all species. "Frequency of Detects" is the number of stations where the metal was
detected at a level above the minimum detection limit (MDL). "No. Stations" is the
number of stations in which a particular fish group was analyzed. A total of 54 fish
samples were analyzed at 33 stations in the small estuaries.
Analyte
All Fish
Total PCBs
Total DDT
Alpha-chlordane
Gamma-chlordane
Trans-nonachlor
Pleuronectiformes
Total PCBs
Total DDT
Alpha-chlordane
Gamma-chlordane
Trans-nonachlor
Perciformes
Total PCBs
Total DDT
Alpha-chlordane
Gamma-chlordane
Trans-nonachlor
"other"
Total PCBs
Total DDT
Alpha-chlordane
Gamma-chlordane
Trans-nonachlor
Mean
(ng/g wet)
43.72
152.74
0.57
1.09
1.68
14.64
36.84
0.10
0.00
0.13
96.90
274.59
1.03
2.24
3.30
0.00
3.10
0.00
0.00
0.00
SD
91.22
446.19
2.17
4.22
5.26
30.69
69.97
0.49
0.00
0.64
117.66
624.45
3.05
5.94
7.28
0.00
4.38
0.00
0.00
0.00
Mean when
Present
84.87
193.86
6.26
11.97
9.26
28.06
44.59
2.37
0.00
3.05
155.03
399.41
8.20
11.97
10.56
0.00
6.20
0.00
0.00
0.00
Minimum
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
Maximum
341.53
2508.90
11.50
22.00
27.07
121.50
254.00
2.37
0.00
3.05
341.53
2508.90
11.50
22.00
27.07
0.00
6.20
0.00
0.00
0.00
Frequency
of Detects/
No.
Stations
17/33
26/33
3/33
3/33
6/33
12/23
19/23
1/23
0/23
1/23
10/16
11/16
2/16
3/16
5/16
0/2
1/2
0/2
0/2
0/2
110
-------
Table 3.2-10. Fish tissue residues of total PCBs, total DDT and additional pesticides
(ng/g wet wt) in Northern California rivers. Alpha-chlordane and Trans-nonachlor were
not detected in the Northern California rivers and thus are not included in this table.
Values for each fish group are the averages of all samples at a station, with samples
consisting of individuals or composites of several individuals. The "All Fish" group is the
overall average combining all species. "Frequency of Detects" is the number of stations
where the metal was detected at a level above the minimum detection limit (MDL). "No.
Stations" is the number of stations in which a particular fish group was analyzed. A total
of 19 fish samples were analyzed at 14 stations in the Northern California rivers.
Analyte
All Fish
Total PCBs
Total DDT
Pleuronectiformes
Total PCBs
Total DDT
Perciformes
Total PCBs
Total DDT
"other"
Total PCBs
Total DDT
Mean
(ng/g wet)
1.53
1.03
0.00
1.07
11.28
0.00
1.11
1.18
SD
3.21
2.39
0.00
1.01
15.95
0.00
2.01
2.60
Mean when
Present
5.36
2.88
0.00
1.60
22.56
0.00
3.00
4.00
Minimum
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
Maximum
11.28
9.00
0.00
2.00
22.56
0.00
4.70
9.00
Frequency
of Detects/
No. Stations
4/14
5/14
0/3
2/3
1/2
0/2
3/12
4/12
Table 3.2-11. Geometric means of tissue lipid content (% wet weight) in composite
samples of three groups offish from California small estuaries and Northern California
rivers. Geometric means with the same superscript are not significantly different
(p<0.001).
Pleuronectiformes
Perciformes
"Other"
Geometric Mean
(% wet weight)
0.505a
1.019b
0.741 a'b
Minimum
0.16
0.28
0.25
Maximum
1.39
2.73
2.81
Number of
Samples
41
18
13
111
-------
3.3 Biotic Condition Indicators
A total of 72 0.1 -m2 benthic samples were taken in California, 47 in the California small
estuaries and 25 in the Northern California rivers. Of these 72 samples, 41 were taken
with grabs and 31 were composited from 16 cores. Most of the core samples were
taken in Northern California because the shallow depth of these small systems
precluded the use of a grab (see Figure 3.1-2). The average penetration of all the
samples was 8.3 cm though six samples in Northern California had a penetration less
than 5 cm. However, there was no significant difference in the number of species per
sample or in the number of individuals per sample in these six samples compared to the
other 19 samples from Northern California (t-test using Iog10 (x+1) transformed data, p >
0.4 in both cases). Therefore, these samples were included in the analysis.
3.3.1 Infaunal Species Richness and Diversity
A total of 552 non-colonial taxa were identified in the California small estuary stations
and Northern California rivers combined. Of these, 522 were found in the California
small estuaries and 94 in the Northern California rivers. An additional 3 colonial taxa
were also identified (e.g., bryozoans on shell fragments). However, because of the
difficulties in standardizing the counts of colonial species, they were excluded from
these counts of total species as well as from other measures of diversity and
abundance. Benthic species richness on a per sample basis ranged from 1 to 95
species per 0.1 m2, and averaged 38.1 species per 0.1 m2 in the California small
estuaries and 10.5 species per 0.1 m2 in the Northern California rivers (Table 3.3-1). Of
the three samples with >80 species per 0.1 m2, two occurred in Drakes Bay just north of
San Francisco Bay and the third occurred in King Harbor in Southern California. All
three of these stations had salinities of 32-33 psu. The maximum species richness in
the Northern California rivers was 35 species per 0.1 m2 in the Russian River, which
also had a salinity of 32 psu. Minimum species richness of 1 species per 0.1 m2
occurred in two Northern California rivers, with both sites having salinities <1 psu. In
the California small estuaries, 5 stations had a richness of <10 species per 0.1 m2.
These sites ranged geographically from northern to central California and with salinities
ranging from 9 to 33 psu.
On an areal basis, 50% of the area of the California small estuaries had a species
richness less than 33.2 species per 0.1 m2 and 90% had a richness less than 69.8
species per 0.1 m2 (Figure 3.3-1). The Northern California rivers had a lower richness,
with 50% of the area of these small estuaries having fewer than 6.3 species per 0.1 m2
and 90% of the area having less than 19.4 species per 0.1 m2 (Figure 3.3-2)
The diversity index H' (log base 2) averaged 3.33 in the small California estuary
stations and 1.46 in the Northern California estuaries (Table 3.3-1). The minimum value
of 0 occurred in the two Northern California stations with a single species. The
minimum value in the California small estuary stations, 1.34, occurred in the Santa Ynez
River, which also had the lowest number of species per sample of the California small
112
-------
estuary stations. The maximum H' value of 5.24 occurred in the Los Angeles Harbor,
while the Northern California maximum of 2.94 occurred in the Albion River, south of
Cape Mendocino. On an areal basis, less than 50% of the area of the California small
estuary stations had an H' of 3.65 while 90% of the area had a value of 5.00 or less
(Figure 3.3-3). In comparison, 50% percent of the area of the Northern California
estuaries had an H' of 1.58 or less while 90% of the area had an H' less than 2.15
(Figure 3.3-4).
3.3.2 Infaunal Abundance and Taxonomic Composition
Benthic density across all of the California small estuaries and Northern California rivers
averaged 2621 individuals per 0.1 m2 and ranged from 7 to 41,582 individuals per 0.1
m2. Average benthic densities were substantially higher in the Northern California sites
than in the rest of the state, 5606 individuals per 0.1 m2 in Northern California rivers
compared to 1033 individuals per 0.1 m2 in the California small estuary stations (Table
3.3-1). The three stations with the highest densities all occurred in Northern California,
two in the Smith River and one in the Little River. The maximum density in the Smith
River equaled 415,820 individuals per m2, one of the highest densities reported for
benthos collected with a 1.0-mm mesh sieve. The amphipods Americorophium
spinicorne and A. salmonis constituted 89% to 97% of the individuals at all three of
these high density stations in Northern California. In the California small estuary
samples, the maximum density of 7383 individuals per 0.1 m2 occurred in Humboldt
Bay. The minimum densities across all the California stations occurred in three sites in
Northern California rivers that had benthic densities <10 individuals per 0.1 m2.
Interestingly, one of these low density sites in the Smith River was adjacent to the site
with the maximum benthic density. Both of these stations had salinities of 9 -10 psu, so
it is unlikely that salinity was the cause for the difference between the two sites. In the
California small estuary stations, a minimum density of 12 individuals per 0.1 m2
occurred in Tomales Bay.
On an areal basis, 50% of the area of the California small estuaries had a benthic
density less than 368 individuals per 0.1 m2 and 90% of the area had a density less than
1857 individuals per 0.1 m2 (Figure 3.3-5). In the Northern California rivers, 50% of the
area had benthic densities less than 2864 individuals per 0.1 m2 and 90% of the area
had densities less than 28,415 individuals per 0.1 m2 (Figure 3.3-6).
The abundance, taxonomic grouping, and classification of the numerically dominant
species in the California small estuaries and in Northern California rivers are shown in
Tables 3.3-2 and 3.3-3, respectively. "Numerically dominant" species are defined as
species having a mean density of ^20 individuals per 0.1 m2. The California small
estuary stations tended to be dominated by annelids while the Northern California rivers
were dominated by crustaceans. Three polychaetes, Streblospio benedicti,
Pseudopolydora paucibranchiata, and Mediomastus sp., were the most abundant taxa
in the California small estuary stations and annelids made up 7 of the 13 numerically
113
-------
dominant species. In contrast, two amphipods, Americorophium spinicorne and A.
salmonis, were the most abundant species in the Northern California sites and
crustaceans made up five of the 10 numerically dominant species. The two populations
of estuaries also differed in the density of the most abundant species, with the densities
of the two Americorophium species in the Northern California rivers more than an order-
of-magnitude greater than the dominant polychaetes in the California small estuary
stations. Another difference was that insects were more abundant in the Northern
California rivers, presumably reflecting the lower salinity of several of the samples (see
Figure 3.1-4).
The benthic species were classified as native, nonindigenous, cryptogenic, or
indeterminate (Tables 3.3-2 and 3.3-3). Cryptogenic species are species of unknown
origin (Carlton, 1996) while indeterminate taxa are those taxa not identified to a
sufficiently low level to classify as native, nonindigenous, or cryptogenic (Lee et al.,
2003). Species were classified using Cohen and Carlton (1995) as the primary
reference supplemented with the report by TN and Associates (2002) that classified the
1999 EMAP benthic species. Of the 552 non-colonial species found across all 72
stations, 28 were nonindigenous (5.1%) and 60 were cryptogenic (10.9%). The
distribution of these invaders was not uniform across the estuaries, with the California
small estuary stations more invaded than the Northern California rivers as measured by
several metrics. All 28 nonindigenous species were found in the California small
estuaries, comprising 5.4% of the 522 species in these stations. In comparison, only 4
nonindigenous specie were found in the Northern California rivers, comprising 4.3% of
the species found in these stations. This difference is more pronounced when
comparing the average percentage of the species per sample composed of
nonindigenous species in the California small estuary stations (8.0%) versus the
Northern California rivers (3.0%). This difference is also seen in the abundance of
nonindigenous species, with nonindigenous species comprising an average of 16.9% of
the individuals per sample in the California small estuaries versus 5.8% in the Northern
California rivers. Finally, nonindigenous species constituted a greater proportion of the
numerically dominant species in the California small estuary stations compared to the
Northern California rivers. The two most abundant species in the California small
estuary stations were nonindigenous, and nonindigenous or cryptogenic species
comprised 6 of the 13 numerically dominant species. In comparison, only one of the 10
numerically dominant species in Northern California rivers was nonindigenous while one
other was cryptogenic.
114
-------
Table 3.3-1: Summary of benthic indices for the California small estuaries (N = 47), and the stations in the Northern
California rivers (N = 25). All indices are per 0.1 -m2 sample.
Benthic Abundance - California small
estuaries
Benthic Abundance - Northern California
rivers
Benthic Species Richness - California small
estuaries
Benthic Species Richness - Northern
California rivers
Benthic H' - California small estuaries
Benthic H' - Northern California rivers
MEAN
1033.0
5605.6
38.1
10.5
3.33
1.46
SD
1442.3
10482.9
23.6
8.2
1.12
0.78
MEDIAN
499.0
1399.0
33.0
7.0
3.24
1.39
RANGE
12-7383
7-41582
5-95
1 -35
1.34-5.24
0-2.94
Ol
-------
Table 3.3-2: Abundance, taxonomic grouping, and classification of the numerically dominant benthic species in the
California small estuaries (N=47). "Numerical dominants" are defined as species with a mean of >= 20 individuals per 0.1-
m2 sample. Taxonomic groupings: A = amphipod, G = gastropod, 0 = oligochaete, P = polychaete, T = tanaid.
Classification of the species: Nat. = native, NIS = nonindigenous, Crypto. = cryptogenic, Indeter. = indeterminate.
Pseudopolydora
paucibranchiata
Streblospio benedicti
Mediomastus sp.
Oligochaeta
Americorophium
spinicorne
Exogone lourei
Grandidierella japonica
Americorophium
stimpsoni
Tryonia imitator
Polydora nuchalis
Leptochelia dubia
Aphelochaeta sp 1
Zeuxo normani
TAXON
P
P
P
O
A
P
A
A
G
P
T
P
T
CLASSIFICATION
NIS
NIS
Indeter.
Indeter.
Nat.
Crypto.
NIS
Nat.
Nat.
Nat.
Crypto.
Nat.
Crypto.
MEAN
(per 0.1 m2)
92.4
75.4
72.4
61.8
52.8
39.7
37.2
32.4
26.2
25.0
24.0
23.3
22.6
SD
427.5
316.8
136.2
211.6
205.7
180.2
124.6
221.3
121.9
127.0
142.6
114.8
120.2
MIN
(per 0.1 m2)
0
0
0
0
0
0
0
0
0
0
0
0
0
MAX
(per 0.1 m2)
2772
1889
668
1348
1011
1151
637
1517
628
815
974
769
811
PERCENT
FREQUENCY
45
28
70
55
21
43
32
9
11
11
23
15
17
CD
-------
Table 3.3-3: Abundance, taxonomic grouping, and classification of the numerically dominant benthic species in the
Northern California rivers (N=25). "Numerical dominants" are defined as species with a mean of >= 20 individuals per 0.1-
m2 sample. Taxonomic groupings: A = amphipod, I = isopod, In = insect, 0 = oligochaete, P = polychaete. Classification:
Nat. = native, NIS = nonindigenous, Crypto. = cryptogenic, Indeter. = indeterminate.
Americorophium
spinicorne
Americorophium
salmonis
Oligochaeta
Eogammarus
confervicolus CMPLX
Neanthes limnicola
Insecta
Streblospio benedicti
Americorophium
stimpsoni
Gnorimosphaeroma
oregonense
Capitella capitata
CMPLX
TAXON
A
A
O
A
P
In
P
A
I
P
CLASSIFICATION
Nat.
Nat.
Indeter.
Nat.
Nat.
Indeter.
NIS
Nat.
Nat.
Crypto.
MEAN
(per 0.1 m2)
3419.6
1213.2
340.3
247.0
92.6
66.7
55.0
54.8
26.4
23.7
SD
8785.7
3258.0
690.8
500.0
236.6
178.5
273.8
228.1
85.9
73.8
MIN
(per 0.1 m2)
0
0
0
0
0
0
0
0
0
0
MAX
(per 0.1 m2)
39700
14728
3219
1953
1004
740
1369
1125
423
345
PERCENT
FREQUENCY
80
40
80
72
44
36
8
12
40
24
-------
Number of Species of Benthic Fauna
California Small Estuaries
100
Figure 3.3 -1. Percent area (and 95% C.I.) of California small estuaries vs. total number
of species of benthic infauna.
Number of Species of Benthic Fauna
Northern California Rivers
100 -
8
< 80 -
£ 60 -I
2
3
O
40 -
20 -
10 15 20 25 30
Number of Species
35
40
Figure 3.3 -2. Percent area (and 95% C.I.) of Northern California rivers vs. total number
of species of benthic infauna.
118
-------
100-
c
0)
u
a. 60
"5 40-
O
20 -
H' Diversity of Benthic Fauna
California Small Estuaries
2 3
H1 Diversity
Figure 3.3 -3. Percent area (and 95% C.I.) of California small estuaries vs. H' diversity
of the benthic infaunal community.
H' Diversity of Benthic Fauna
Northern California Rivers
100 -
< 80 -
60
•2 40 -
I
5 20 ^
0.5
1.5 2
H' Diversity
2.5
3.5
Figure 3.3 -4. Percent area (and 95% C.I.) of Northern California rivers vs. H' diversity
of the benthic infaunal community.
119
-------
Abundance of Benthic Fauna
California Small Estuaries
-Cumulative Percent
95% Confidence Interval
0 1000 2000 3000 4000 5000 6000
Abundance
7000 8000
Figure 3.3 -5. Percent area (and 95% C.I.) of California small estuaries vs. total
abundance of benthic infauna.
Abundance of Benthic Fauna
Northern California Rivers
100 -
ro
s>
<
S.
I
O
80 -
60 -
40 -
20 -
-Cumulative Percent
- 95% Confidence Interval
0 5000 10000 15000 20000 25000 30000 35000 40000 45000
Abundance
Figure 3.3 -6. Percent area (and 95% C.I.) of Northern California rivers vs. total
abundance of benthic infauna.
120
-------
3.3.3 Demersal Species Richness and Abundance
An attempt was made to quantify fish abundance and composition at all stations by
sampling with a 16-foot bottom otter trawl. There was a total of 37 successful trawls in
the 50 California small estuary stations but only 2 successful trawls among the 30
Northern California river stations largely because of the small size of these rivers.
Trawls were pulled at an average speed of 2.01 knots (SD = 0.27) with a range of 1.0 to
3.1 knots. Trawl duration averaged 9.79 minutes (SD = 1.06) with a range of 5 to 12
minutes. Because the missing stations did not appear to be randomly distributed and
because of the differences in trawl speed and duration, analysis of the fish trawl data is
limited to summary statistics and species composition and no CDFs are presented.
A total of 57 fish species were collected in the California small estuaries with no
additional species collected from the trawls in the Northern California rivers. Species
richness averaged 5.57 species per trawl in the California small estuaries with a
maximum of 17 species in a single trawl in Drakes Bay (Table 3.3-4). Though based on
only two trawls, species richness averaged 3.5 species per trawl in the Northern
California rivers (Table 3.3-5). Total fish abundance averaged 70.32 individuals per
trawl in the California small estuaries with a maximum of 496 individuals in a single trawl
in Bodega Bay (Table 3.3-4). English sole (Pleuronectes vetulus) and the speckled
sanddab (Citharichthys stigmaeus) constituted 46.6% and 23.2%, respectively, of the
individuals in this Bodega Bay trawl. In the two Northern California river trawls, total
abundance averaged 26.0 individuals per trawl (Table 3.3-5) with a maximum of 35
individuals per trawl.
The ten most abundant species in the California small estuaries are listed in Table 3.3-
4. Averaged across all the California small estuary stations, the English sole
(Pleuronectes vetulus) and the speckled sanddab (Citharichthys stigmaeus) were the
two most abundant species, making up more than 50% of the individuals. However,
there was a strong latitudinal pattern in the distribution of the dominant species.
Citharichthys sordidus, Citharichthys stigmaeus, Cymatogaster aggregata,
Hyperprosopon anale, Ophiodon elongatus, Pleuronectes vetulus, Seriphus politus, and
Spirinchus thaleichthys all occurred predominately or exclusively in stations north of
Point Conception (34.449 degrees north latitude). In comparison, Genyonemus lineatus
and Urolophus halleri only occurred in stations south of Point Conception. As in the
other stations north of Point Conception, Citharichthys stigmaeus and Pleuronectes
vetulus were the two most abundant species in the Northern California river stations
(Table 3.3-5).
121
-------
Table 3.3.-4. Mean number of fish captured per trawl, mean number of fish species per
trawl, and mean abundance of the ten numerically dominant fish species in the
California small estuaries (N=37). Relative abundance is the percentage the species
makes up of the total abundance. Frequency is the number or percent of trawls in which
each species was captured. SD = standard deviation. NA = not applicable.
Parameter/
Species
Total
abundance
Total species
Citharichthys
stigmaeus
Pleuronectes
vetulus
Genyonemus
lineatus
Ophiodon
elongatus
Seriphus
politus
Urolophus
halleri
Spirinchus
thaleichthys
Citharichthys
sordidus
Cymatogaster
aggregate
Hyperprosopon
anale
Common
name
NA
NA
Speckled
sanddab
English
sole
White
croaker
Lingcod
Queenfish
Round
stingray
Longfin
smelt
Pacific
sanddab
Shiner
perch
Spotfin
seaperch
Mean per
trawl
70.32
5.57
19.16
17.70
4.16
3.27
3.22
3.05
2.22
1.89
1.89
1.46
SD
113.7
8
3.85
43.23
49.04
14.94
8.84
16.18
10.81
12.98
7.94
9.87
6.92
Max
496
17
194
231
76
40
97
58
79
47
60
42
Relative
Abundance
(%)
NA
NA
27.2
25.2
5.9
4.7
4.6
4.3
3.2
2.7
2.7
2.1
Frequency
(% Frequency)
36
(97.3%)
36
(97.3%)
15
(40.5%)
9
(24.3%)
9
(24.3%)
8
(21.6%)
3
(8.1%)
4
(10.8%)
3
(8.1%)
7
(18.9%)
6
(16.2%)
6
(16.2%)
122
-------
Table 3.3.-5. Mean number of fish captured per trawl, mean number of fish species per
trawl, and mean abundance of the ten numerically dominant fish species in the Northern
California rivers (N=2). Relative abundance is the percentage the species makes up of
the total abundance. Frequency is the number or percent of trawls in which each
species was captured. SD = standard deviation. NA = not applicable.
Parameter/
Species
Total
abundance
Total species
Citharichthys
stigmaeus
Pleuronectes
vetulus
Sebastes
mystinus
Ophiodon
elongatus
Common name
NA
NA
Speckled
sanddab
English sole
Blue rockfish
Lingcod
Mean per
trawl
26.00
3.50
22.00
2.50
1.00
0.50
SD
12.73
0.71
9.90
2.12
0.00
0.71
Max
35
4
29
4
1
1
Relative
Abundance
(%)
NA
NA
84.6
9.6
3.8
1.9
Frequency
(%
Frequency)
2
(100%)
2
(100%)
2
(100%)
2
(100%)
2
(100%)
1
(50%)
123
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