USGS Publications on San Francisco Bay

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Aguado, E., Cayan, D.R, Reece, B., and Riddle, L., 1993, Patterns of orographic uplift in the Sierra Nevada and their relationship to upper-level atmospheric circulation, in Redmond, K.T., and Tharp, V.L., eds., Proceedings of the Ninth Annual Pacific Climate (PACLIM) Workshop: PACLIM, Asilomar, Calif., April 21-24, 1992, p. 153-164.

Alfaro, E.J., Gershunov, A., and Cayan, D., 2006, Prediction of summer maximum and minimum temperature over the central and western United States: The role of soil moisture and sea surface temperature. J. Climate, 19(8), 1407-1421.

Allison, D., Hampton, M., and Jaffe, B., 2003, Preliminary analysis of cores from north San Francisco Bay, California. U.S. Geological Survey Open-File Report 03-111 [URL http://geopubs.wr.usgs.gov/open-file/of03-111/].

Alpine, A.E., 1983, Use of in-vivo fluorescence to size fractionate phytoplankton biomass: San Francisco, San Francisco State University, Masters thesis, 43 p.

Alpine, A.E., and Cloern, J.E., 1985, Differences in-vivo fluorescence yield between three phytoplankton size classes: Journal of Plankton Research, v. 7, p. 381-390.

Alpine, A.E., and Cloern, J.E., 1988, Phytoplankton growth rates in a light-limited environment, San Francisco Bay: Marine Ecology Progress Series, v. 44, p. 167-173.

Alpine, A.E., and Cloern, J.E., 1992, Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary: Limnology and Oceanography, v. 37, p. 946-955.

Alpine, A.E., Cloern, J.E., and Cole, B.E., 1981, Plankton studies in San Francisco Bay, 1, chlorophyll distributions and hydrographic properties of the San Francisco Bay estuary, July 1977-December 1979: U.S. Geological Survey Open-File Report 81-213, 150 p.

Alpine, A.E., Wienke, S.M., Cloern, J.E., and Cole, B.E., 1988, Plankton studies in San Francisco Bay, IX, chlorophyll distributions and hydrographic properties of south San Francisco Bay, 1984-1986: U.S. Geological Survey Open-File Report 88-319, 86 p.

Alpine, A.E., Wienke, S.M., Cloern, J.E., Cole, B.E., and Wong, R.L.J., 1985, Plankton studies in San Francisco Bay, VIII, chlorophyll distributions and hydrographic properties of south San Francisco Bay, 1983: U.S. Geological Survey Open-File Report 85-196, 58 p.

Ambler, J.W., Cloern, J.E., and Hutchinson, A., 1985, Seasonal cycles of zooplankton from San Francisco Bay: Hydrobiologia, v. 129, p. 177-197.

Arnal, R.E., Quinterno, P.J., Conomos, T.J., and Gram, R., 1980, Trends in the distribution of Recent Foraminifera in San Francisco Bay: Cushman Foundation Special Publication, v. 19, p. 17-39.

Athearn, N.D., Goodenough, K., Takekawa, J.Y., Miles, A.K., Saiki, M.K., Spring, S., Mejia, F., Shellenbarger, G.G., and Schoellhamer, D.H., 2005,  Napa-Sonoma marshes pond 3, hydrologic and biotic changes in a salt pond following breaching: Proceedings of the 7th biennial State-of-the-Estuary Conference, Oakland, California, October 4-6, 2005, p. 59.

Athearn, N.D., and Takekawa, J.Y., 2006, Avian Data Summaries and Analyses from Short-term Data Needs, 2003-2005,  Unpublished Report, U.S. Geological Survey, Vallejo, CA. 183 p.

Atwater, B.F., 1979, Ancient processes at the site of southern San Francisco Bay, movement of the crust and changes in sea level, in Conomos, T.J., ed., San Francisco Bay - The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 31-45.

Atwater, B.F., and Belknap, D.F., 1980, Tidal-wetland deposits of the Sacramento - San Joaquin Delta, California, in Field, M.E., Buoma, A.H., Coburn, I.P., Douglas, R.G., and Ingle, J.C., Jr., eds., Quaternary Depositional Environments of the Pacific Coast: Society of Economic Paleontologists and Mineralogists, Pacific Coast Paleogeography Symposium, v. 4, p. 89-103.

Atwater, B.F., Conrad, S.G., Dowden, J.N., Hedel, C.W., MacDonald, R.L., and Savage, W., 1979, History, landforms, and vegetation of the estuary's tidal marshes, in Conomos, T.J., ed., San Francisco Bay - The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 347-386.

Atwater, B.F., and Hedel, C.W., 1976, Distribution of seed plants with respect to tide levels and water salinity in the natural tidal marshes of the northern San Francisco Bay estuary, California: U.S. Geological Survey Open-File Report 76-389, 41 p.

Atwater, B.F., Hedel, C.W., and Helley, E.J., 1977, Late Quaternary depositional history, Holocene sea-level changes, and vertical crustal movement, southern San Francisco Bay: U.S. Geological Survey Professional Paper 1014, 15 p.

Bachman, R.W., Cloern, J.E., Hecky, R.E., and Schindler, D.W. (editors), 2006, Eutrophication of Freshwater and Marine Ecosystems, Limnology and Oceanography, Special Issue 51: 351-800.

Baines, S.B., Fisher, N.S., and Stewart, A.R., 2002, Assimilation and retention of selenium and other trace elements from crustacean food by juvenile striped bass (Morone saxatilis), Limnology and Oceanography, v. 47, no. 3, p. 646-655.

Bales, R., Molotch, N., Painter, T., Dettinger, M., Rice, R., and Dozier, J., 2006, Mountain hydrology of the western US: Water Resources Research, W08432, doi:10.1029/2005WR004387, 13 p.

Barad, M.F., Schladow, S.G., Warner, J.C., and Schoellhamer, D.H., 2001, CISNet San Pablo Bay Network of Environmental Stress Indicators: The CISNet Hydrodynamic Database: Proceedings of the 5th biennial State of the Estuary Conference, San Francisco, Calif., October 9-11, 2001, p. 112.

Baylosis, J.I., Cole, B.E., and Cloern, J.E., 1998, Studies of the San Francisco Bay, California, estuarine ecosystem. pilot regional monitoring program results, 1997: U.S. Geological Survey Open-File Report 98-168, 209 p.

Baylosis, J.I., Edmunds, J.L, Cole, B.E., and Cloern, J.E., 1997, Studies of the San Francisco Bay, California estuarine ecosystem: pilot regional monitoring results, 1996: U.S. Geological Survey Open-File Report 97-598, 203 p.

Bearman, J., Foxgrover, A., Friedrichs, C., and Jaffe, B., 2006, Factors controlling tidal flat morphology in South San Francisco Bay, [abs.]: South Bay Science Symposium, "South Bay Salt Ponds, Bay and Watershed Research," San Jose, Calif., June 6, 2006.

Bearman, J., Foxgrover, A., Friedrichs, C., and Jaffe, B., 2006, Factors controlling tidal flat morphology in South San Francisco Bay, Eos Trans. AGU, 87(52), Fall Meet. Suppl., Abstract H33B-1498

Bergamaschi, B.A., Baston, D.S., Crepeau, K.L., and Kuivila, K.M., 1998, Determination of pesticides associated with suspended sediments in the San Joaquin River, CA using gas chromatography-ion trap mass spectrometry: Toxicological and Environmental Chemistry, v. 69, p. 305-319.

Bergamaschi, B.A., Downing, B.D., Wheeler, G.A., Schoellhamer, D.H., Ganju, N., Fram, M.S., Erickson, D.E., Kendall, C., Bemis, B.E., Stepanauskas, R., Hollibaugh, J.T., and Fujii, R., 2003, Quantifying the contributions of tidal wetlands to dissolved organic material in the San Francisco Estuary, California, USA: Proceedings of the 17th Biennial Conference of the Estuarine Research Federation, Seattle, Washington, September 14-18, 2003, p. 13.

Bergamaschi, B.A., Crepeau, K.L., and Kuivila, K.M., 1997, Pesticides associated with suspended sediments in the San Francisco Bay estuary, California: U.S. Geological Survey Open-File Report 97-24.

Bergamaschi, B.A., Kuivila, K.M., and Fram, M.S., 1999, Pesticides associated with suspended sediments in the San Francisco Bay during the first flush, December, 1995, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program - Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2 - Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 23-34.

Bergamaschi, B.A., Kuivila, K.M., and Fram, M.S., 2001, Pesticides associated with suspended sediments entering San Francisco Estuary following the first major storm of water year 1996, Estuaries, v. 24(3), p. 368-380.

Bergfeld, L.G., and Schoellhamer, D.H., 2003, Comparison of salinity and temperature at continuous monitoring stations and nearby monthly measurement sites in San Francisco Bay: IEP Newsletter, v. 16, no. 3, p. 5-11.

Bradford, W.L., and Luoma, S.N., 1980, Some perspectives on heavy metal concentrations in shellfish and sediment in San Francisco Bay, California, in Baker, R.A., ed., Contaminants and Sediments, v. 2, Ann Arbor Science Publishers, Inc., p. 501-532.

Brennan, M.L., Schoellhamer, D.H., Burau, J.R., and Monismith, S.G., 2002, Tidal asymmetry and variability of bed shear stress and sediment bed flux at a site in San Francisco Bay, USA, in Winterwerp, J.C. and Kranenburg, C., ed., Fine Sediment Dynamics in the Marine Environment: Elsevier Science B.V., p. 93-108.

Brown, C.L., and Luoma, S.N., 1995, Energy-related selenium and vanadium contamination in San Francisco Bay, California - effects on biological resources, in Tenth McKelvey Forum on Energy and the Environment - Application of Geosciences to Decision Making: U.S. Geological Survey Circular 1108, p. 91-93.

Brown, C.L., and Luoma, S.N., 1998, Metal trends and effects in Potamocorbula amurensis in north San Francisco Bay: Interagency Ecological Program Newsletter, v. 11, no. 2, p. 33-35.

Brown, C.L., and Luoma, S.N., 1999, Metal trends and effects in Potamocorbula amurensis in north San Francisco Bay, in Morganwalp, D.W., and Buxton, H.T., eds.  U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2—Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 17-23.

Brown, C.L., Parchaso, F., Thompson, J.K., and Luoma, S.N., 2003,  Assessing toxicant effects in a complex estuary: a case study of effects of silver on reproduction in the bivalve Potamocorbula amurensis in San Francisco Bay : Human and Ecological Risk Assessment, v. 9, no. 1, p. 95-119.

Buchanan, P.A., 1999, Specific conductance, water temperature, and water level data, San Francisco Bay, California, water year 1998: Interagency Ecological Program Newsletter, v. 12, no. 4, p. 46-51.

Buchanan, P.A., 2000, Specific conductance, water temperature, and water level data from San Francisco Bay, California, in water year 1999: Interagency Ecological Program Newsletter, v. 13, no. 3, p. 17-20.

Buchanan, P.A., 2002, Water level, specific conductance, and water temperature data, San Francisco Bay, California, for Water Year 2000: Interagency Ecological Program Newsletter, v. 15, no. 1, p. 22-26.

Buchanan, P.A., 2003, Specific-conductance, water-temperature, and water-level data, San Francisco Bay, California, for water years 2001-2002: Interagency Ecological Program Newsletter, v. 16, no. 4, p. 25-30.

Buchanan, P.A., 2004, Specific conductance and water temperature data for San Francisco Bay, California, for Water Year 2003: Interagency Ecological Program Newsletter, v. 17, no. 3, p. 11-14.

Buchanan, P.A., 2005, Specific conductance and water temperature data for San Francisco Bay, California, for Water Year 2004: Interagency Ecological Program Newsletter, v. 18, no. 3, p. 2-6.

Buchanan, P.A., and Ganju, N.K., 2002, Summary of suspended-sediment concentration data, San Francisco Bay, California, water year 2000: USGS Open file report 01-100, 56 p.

Buchanan, P.A., and Ganju, N.K., 2003, Summary of suspended-sediment concentration data, San Francisco Bay, California, water year 2001: U.S. Geological Survey Open-File Report 03-312.

Buchanan, P.A., and Ganju, N.K., 2004. Summary of suspended-sediment concentration data, San Francisco Bay, California, Water Year 2002: U.S. Geological Survey Open File Report 2004-1219.

Buchanan, P.A., and Ganju, N.K., 2005, Summary of suspended-sediment concentration data in San Francisco Bay, California, water year 2003: U.S. Geological Survey Data Series 113.

Buchanan, P.A., and Lionberger, M.A., 2006, Summary of suspended-sediment concentration data in San Francisco Bay, California, water year 2004: U.S. Geological Survey Data Series 226, 49 p.

Buchanan, P.A., and Ruhl, C.A., 2000, Summary of suspended-solids concentration data, San Francisco Bay, California, water year 1998: U.S. Geological Survey Open File Report 00-88, 41 p.

Buchanan, P.A., and Ruhl, C.A., 2001, Summary of suspended-sediment concentration data, San Francisco Bay, California, water year 1999: U.S. Geological Survey Open File Report 01-100, 56 p.

Buchanan, P.A., and Schoellhamer, D.H., 1995, Summary of suspended-solids concentration data, central and south San Francisco Bay, California, water years 1992 and 1993: U.S. Geological Survey Open-File Report 94-543, 15 p.

Buchanan, P.A., and Schoellhamer, D.H., 1996,  Summary of suspended-solids concentration data, San Francisco Bay, California, water year 1995: U.S. Geological Survey Open-File Report 96-591, 40 p.

Buchanan, P.A., and Schoellhamer, D.H., 1998, Summary of suspended-solids concentration data in San Francisco Bay, California, water year 1996: U.S. Geological Survey Open-File Report 98-175, 59 p.

Buchanan, P.A., and Schoellhamer, D.H., 1999, Summary of suspended-solids concentration data in San Francisco Bay, California, water year 1997: U.S. Geological Survey Open-File Report 99-189, 52 p.

Buchanan, P.A., and Ganju, N.K., 2002, Summary of suspended-sediment concentration data, San Francisco Bay, California, water year 2000: U.S. Geological Survey Open File Report 02-146.

Buchanan, P.A., Schoellhamer, D.H., and Sheipline, R.C., 1996,  Summary of suspended-solids concentration data, San Francisco Bay, California, water year 1994: U.S. Geological Survey Open-File Report 95-776, 48 p.

Burau, J.R., and Cheng, R.T., 1988, Predicting tidal currents in San Francisco Bay using a spectral model, in Abt, S.R., and Gessler, J., eds., Proceedings American Society of Civil Engineers National Hydraulic Engineering Conference: Colorado Springs, Colo., p. 634-639.

Burau, J.R., and Cheng, R.T., 1989, A general method for generating bathymetric data for hydrodynamic computer models: U.S. Geological Survey Open-File Report 89-28, 41 p.

Burau, J.R., and Cheng, R.T., 1989, A vertically averaged spectral model for tidal circulation in estuaries, Part 1, model formulation: U.S. Geological Survey Open-File Report 88-4126, 29 p.

Burau, J.R., Gartner, J.W., and Stacey, M., 1998, Results from the hydrodynamic element of the 1994 entrapment zone study in Suisun Bay: Interagency Ecological Program for the San Francisco Bay/Delta Estuary Technical Report 56, p. 13-55.

Burau, J.R., Monismith, S.G., Stacey, M.T., Oltmann, R.N., Lacy, J.R., Schoellhamer, D.H., 1999, Recent research on the hydrodynamics of the Sacramento - San Joaquin River Delta and north San Francisco Bay: Interagency Ecological Program Newsletter, v. 11, no. 2, p. 45-55.

Burau, J.R., Stacey, M., and Gartner, J.W., 1995, Preliminary results from the hydrodynamic element of the 1994 entrapment zone study: Interagency Ecological Program for the Sacramento - San Joaquin Estuary Newsletter, Autumn 1995, p. 12-17.

Cacchione, D.A., Gardner, J.V., Chavez, P.F., Chin, J.L., Dartnell, P., and Velasco, M., 1997, The seafloor of central San Francisco Bay, California [abs]: American Geophysical Union, Fall Meeting, San Francisco, December 8-12, 1997.

Caffrey, J.M., Cole, B.E., Cloern, J.E., Rudek, J.R., Tyler, A.C., and Jassby, A.D., 1994, Studies of the San Francisco Bay, California, estuarine ecosystem: pilot regional monitoring program results, 1993: U.S. Geological Survey Open-File Report 94-82, 411 p.

Caffrey, J.M., Grenz, C., and Cloern, J.E., 1998,  Changes in production and respiration during a spring phytoplankton bloom in San Francisco Bay, California, USA: implications for net ecosystem metabolism: Marine Ecology Progress Series, v. 172, p. 1-12.

Caffrey, J., Hammond, D., Kuwabara, J., Miller, L., and Twilley, R., 1996, Benthic processes in San Francisco Bay: the role of organic inputs and bioturbation, in Hollibaugh, J.T., ed., San Francisco Bay  - The Ecosystem: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 425-442.

Cain, D.J., and Luoma, S.N., 1985, Copper and silver accumulation in transplanted and resident clams (Macoma balthica) in south San Francisco Bay: Marine Environmental Research, v. 15, p. 115-135.

Cain, D.J., and Luoma, S.N., 1986, Effect of seasonally changing tissue weight on trace metal concentrations in the bivalve Macoma balthica in San Francisco Bay: Marine Ecology Progress Series, v. 28, p. 209-217.

Cain, D.J., and Luoma, S.N., 1990, Influence of seasonal growth, age, and environmental exposure on Cu and Ag in a bivalve indicator, Macoma balthica, in San Francisco Bay: Marine Ecology Progress Series, v. 60, p. 45-55.

Cain, D.J., Thompson, J.K., and Luoma, S.N., 1987, The effect of differential growth on spatial comparisons of copper content of a bivalve indicator, in Lindberg, S.E., and Hutchinson, T.C., eds., Heavy Metals in the Environment: Edinburgh CEP Consultants Ltd., p. 455-457.

Cain, D. J., Parchaso, F., Thompson, J.K., Luoma, S.N., Lorenzi, A.H., Moon, E., Shouse, M. K., Hornberger, M.I., and J.L. Dyke, 2006, Near-Field Receiving Water Monitoring of Trace Metals and a Benthic Community Near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California: 2005, U.S. Geological Survey Open File Report 2006-1152, Menlo Park, California, 128p.

Canuel, E.A., and Cloern, J.E., 1996, Regional differences in the origins of organic matter in the San Francisco Bay ecosystem: evidence from lipid biomarkers, in Hollibaugh, J.T., ed., San Francisco Bay: The Ecosystem: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 305-324.

Canuel, E.A., Cloern, J.E., Ringelberg, D.B., Guckert, J.B., and Rau, G.H., 1995, Molecular and isotopic tracers used to examine sources of organic matter and its incorporation into the food webs of San Francisco Bay: Limnology and Oceanography, v. 40, p. 67-81.

Cappiella, K., Malzone, C., Smith, R., and Jaffe, B., 1999, Sedimentation and bathymetry changes in Suisun Bay, 1867-1990: U.S. Geological Survey Open-File Report 99-563. [poster]

Carlson, P.R., Alpha, T.R., and McCulloch, D.S., 1970, The floor of central San Francisco Bay: Mineral Information Service, California Division of Mines and Geology, v. 23, no. 5, p. 97-107.

Carlson, P.R., and McCulloch, D.S., 1974, Aerial observations of suspended sediment plumes in San Francisco Bay and the adjacent Pacific Ocean: U.S. Geological Survey, Journal of Research, v. 2, p. 519-526.

Carlton, J.T., Thompson, J.K., Schemel, L.E., and Nichols, F.H., 1990, The remarkable invasion of San Francisco Bay (California, USA) by the Asian clam Potamocorbula amurensis, I, Introduction and dispersal: Marine Ecology Progress Series, v. 66, p. 81-94.

Casulli, V., Bertolazzi, E., and Cheng, R.T., 1993, TRIM_3D: a three-dimensional model for accurate simulation of shallow water flow, in National Conference on Hydraulic Engineering, 1993, Proceedings: American Society of Civil Engineers, San Francisco, Calif., July 1993, p. 1,988-1,993.

Casulli, V., and Cheng, R.T., 1992, A semi-implicit finite difference model for three-dimensional tidal circulation, in Spaulding M., and others, eds., Estuarine and Coastal Modeling: American Society of Civil Engineers, Tampa, Fla., p. 620-631.

Casulli, V., and Cheng, R.T., 1992, Semi-implicit finite difference methods for three-dimensional shallow water flow: International Journal for Numerical Methods in Fluids, v. 15, p. 629-648.

Casulli, V., and Cheng, R.T., 1994, Solutions of primitive equations for three-dimensional tidal circulation, in Third International Conference on Estuarine and Coastal Modeling, Proceedings: American Society of Civil Engineers, Chicago, Ill., September 1993, p. 396-406

Casulli, V., Cheng, R.T., and Bulgarelli, U., 1984, Eulerian - Lagrangian solution of convection dominated diffusion problems: Proceedings of 2nd Annual Conference on Numerical Methods for Non-Linear Problems, Barcelona, Spain, v. 2, p. 962-971

Catts, G.P., Khorram, S., Cloern, J.E., Knight, A.W., and DeGloria, S.D., 1985, Remote sensing of tidal chlorophyll - variations in estuaries: International Journal of Remote Sensing, v. 6, no. 11, p. 1,685-1,706.

Cayan, D.R., 1996, Climate variability and snowpack in the western United States: Journal of Climate, v. 9, p. 928-948.

Cayan, D.R., Bromirski, P., Hayhoe, K., Tyree, M., Dettinger, M., and Flick, R., 2006, Projecting future sea level: Report to California Energy Commission and California Environmental Protection Agency, 30 p.

Cayan, D.R., Dettinger, M.D., Caprio, J.M., Kammerdiener, S.A., and Peterson, D.H., 2001, Reply to Comments on “Changes in the Onset of Spring in the Western United States”; by D. Lilly: Bulletin American Meterological Society, v. 82, p. 2,265-2,266.

Cayan, D.R., Dettinger, M.D., Diaz, H.F., and Graham, N., 1997, Decadal variability of precipitation over western North America: American Meteorological Society, 8th Symposium on Global Change Studies, Long Beach, Calif., p. 34-35.

Cayan, D.R., Dettinger, M.D., Diaz, H.F., and Graham, N., 1998,  Decadal variability of precipitation over western North America: Journal of Climate, v. 11, p. 3,148-3,166.

Cayan, D., Dettinger, M., Stewart, I., and Knowles, N., 2005, Recent changes toward earlier springs---Early signs of climate warming in western North America: Watershed Management Council Networker, 13, Spring 2005, 3-7.

Cayan, D.R., Kammerdiener, S.A., Dettinger, M.D., Caprio, J.M., and Peterson, D.H., 2001,  Changes in the Onset of Spring in the Western United States: Bulletin of the American Meteorological Society, v. 82, no. 3, p. 399-415.

Cayan, D.R., Maurer, E., Dettinger, M., Tyree, M., Hayhoe, K., Bonfils, C., Duffy, P., and Santer, B., 2006, Climate scenarios for California: Report to California Energy Commission and California Environmental Protection Agency, 40 p.

Cayan, D.R., McClain, D.R., Nichols, W.D., and DiLeo-Stevens, J., 1991, The monthly climate time series data for the Pacific Ocean and western Americas: U.S. Geological Survey Open-File Report 91-92, 380 p.

Cayan, D.R., Miller, A., Barnett, T., Graham, N., Ritchie, J., and Oberhuber, J.F., 1995, Seasonal-interannual fluctuations in surface temperature over the Pacific: effects of monthly winds and heat fluxes, in Natural Climate Variability on Decade-to-Century Time Scales: Washington, D.C., National Academy Press, p. 133-148.

Cayan, D.R., and Peterson, D.H., 1989, The influence of north Pacific atmospheric circulation on streamflow in the west, in Peterson, D.H., ed., Climate Variability on the eastern Pacific and western North America: Geophysical Monograph 55, Geophysical Union, p. 375-397.

Cayan, D.R., and Peterson, D.H., 1993, Spring climate and salinity in the San Francisco Bay estuary: Water Resources Research, v. 29, no. 2, p. 293-303.

Cayan, D.R., Peterson, D.H., Riddle, L., Dettinger, M.D., and Smith, R.E., 1997, The spring runoff pulse from the Sierra Nevada: Interagency Ecological Program Newsletter, Summer 1997, p. 25-28.

Cayan, D.R., Peterson, D.H., Riddle, L., Dettinger, M.D., and Smith, R., 1999,  The spring runoff pulse from the Sierra Nevada: American Meteorological Society, 14th Conference on Hydrology, Dallas, Tex., January 1999, p. 77-79.

Cayan, D.R., Redmond, K.T., and Riddle, L.G., 1999, ENSO and hydrologic extremes in the western United States: Journal of Climate, v. 12, p. 2,881-2,893.

Cayan, D.R., and Riddle, L., 1992, Atmospheric circulation and precipitation in the Sierra Nevada, in Herrmann, R., ed., 28th Annual Conference and Symposium: American Water Resources Association, Reno, Nevada, p. 711-720.

Cayan, D.R., and Webb, R.H., 1992, El Nino/southern Oscillation and streamflow in the western United States, in Diaz, H.F., and Markgraf, V., eds., El Nino - Historical and Paleoclimatic Aspects of the Southern Oscillation: Cambridge, Cambridge University Press, p. 29-68.

Chadwick, D.B., Largier, J.L., and Cheng, R.T., 1996, The role of thermal stratification in tidal exchange at the mouth of San Diego Bay, in Aubrey, D.G., and Friedrichs, C.T., eds., Buoyancy Effects on Estuaries and Coastal Dynamics: American Geophysical Union Coastal and Estuarine Studies, v. 53, p. 155-174.

Chauvaud, L., Thompson, J.K., Cloern, J.E., and Thouzeau, G., 2003, Clams as CO₂ generators: the Potamocorbula amurensis example in San Francisco Bay: Limnology and Oceanography, v. 48, no. 6, p. 2,086-2,092.

Cheng, R.T., 1978, Comparison of a few recording current meters in San Francisco Bay, CA: Proceedings, Conference on Current Measurements, Delaware University, Newark, N.J., p. 293-301.

Cheng, R.T., 1980, Modeling of environmental hydrodynamics and field data requirements: Proceedings, 3rd International Conference on Finite Elements in Flow Problems, Banff, Canada, p. 43-53.

Cheng, R.T., 1982, Modeling of tidal and residual circulation in San Francisco Bay, California: Proceedings, Seminar on 2-D Flows, HEC Report, U.S. Army Corps of Engineers, Davis, Calif., July 1981, p. 172-185.

Cheng, R.T., 1983, Euler-Lagrangian computation for estuarine hydrodynamics, in Taylor, C., and others, eds., Proceedings, 3rd International Conference on Numerical Methods in Laminar and Turbulent Flows: Swansea, Wales Pineridge Press, p. 341-352.

Cheng, R.T., 1986, Modeling of estuarine hydrodynamics - a mixture of art and science: Proceedings, 3rd International Symposium on River Sedimentation, Jackson, Wyo., p. 1,468-1,475.

Cheng, R.T., 1988, Eulerian and Lagrangian modeling of estuarine hydrodynamics, in Kjerfve B., ed. Hydrodynamics of Estuaries, v. 1: Boca Raton, Fla., CRC Press Inc., p. 149-159.

Cheng, R.T., ed., 1990, Residual currents and long-term transport: Coastal and Estuarine Studies, v. 38: New York, Springer-Verlag, 544 p.

Cheng, Ralph T., 1995, Viewpoints and practices - numerical modeling of 3-D estuarine hydrodynamics: Advances in Hydro-Science And Engineering, v. II, Part B, p. 1,361-1,367.

Cheng, R.T., and Burau, J.R., 1988, System considerations in numerical modeling of estuarine problems, in Niki, H., and Kawahara, M., eds., Computational Methods in Flow Analysis: Proceedings, International Conference on Computational Method in Flow Analysis, Okayama, Japan, 1988, p. 1,025-1,032.

Cheng, R.T., Burau, J.R., and Gartner, J.W., 1991, Interfacing data analysis and numerical modeling for tidal hydrodynamic phenomena, in Parker, B.B., ed., Tidal Hydrodynamics: New York, John Wiley, p. 201-219.

Cheng, R.T., and Casulli, V., 1982, On Lagrangian currents with applications in south San Francisco Bay, California: Journal of Water Resources Research, v. 18, no. 6, p. 1,652-1,662.

Cheng, R.T., and Casulli, V., 1992, Dispersion in tidally averaged transport equation, in Prandle, D., ed., Dynamics and Exchanges in Estuaries and the Coastal Zone: Coastal and Estuarine Studies, American Geophysical Union, v. 38, p. 409-428.

Cheng, R.T., and Casulli, V., 1992, Tidal, residual, intertidal mudflat (TRIM) model using a semi-implicit Eulerian-Lagrangian method: U.S. Geological Survey Open-File Report 92-62, 43 p.

Cheng, R.T., and Casulli, V., 1996, Modeling the periodic stratification and gravitational circulation in San Francisco Bay, in Spaulding, M., and Cheng, R.T., eds., Estuarine and Coastal Modeling: American Society of Civil Engineers, San Diego, Calif., October 1995, p. 240-254.

Cheng, R.T., Casulli, V., and Gartner, J.W., 1993, Tidal, residual, intertidal mudflat (TRIM) model and its applications to San Francisco Bay, California: Estuarine, Coastal, and Shelf Science, v. 36, p. 235-280.

Cheng, R.T., Casulli, V., and Milford, S.N., 1984, Eulerian-Lagrangian solution of the convection-dispersion equation in natural coordinates: Water Resources Research, v. 20, no. 7, p. 944-952.

Cheng, R.T., and Conomos, T.J., 1980, Studies of San Francisco Bay by the U.S. Geological Survey: Proceedings, 26th Annual Meeting of the Institute of Environmental Sciences, Philadelphia, Penn., p. 299-303.

Cheng, R.T., Feng, S., and Xi, P., 1986, On Lagrangian residual ellipse, in van de Kreeke, J., ed., Symposium on Physics of Shallow Estuaries and Bays: Springer-Verlag Publishers, p. 102-113.

Cheng, R.T., Feng, S., and Xi, P., 1989, On inter-tidal transport equation, in Circulation in Estuaries: The College of William and Mary Charter Day Symposium.

Cheng, R.T., Feng, S., and Xi, P., 1989, On inter-tidal transport equation, in Neilson, Kuo, and Brubaker, eds., Estuarine Circulation: Totowa, N.J., Humana Press, p. 133-156.

Cheng, R.T., and Gartner, J.W., 1979, A microcomputer based system for current-meter data acquisition, reprinted from: Proceedings of Oceans, September 1979, p. 288-291.

Cheng, R.T., and Gartner, J.W., 1980, Working notes on current meter deployment, recovery, maintenance, and data processing for San Francisco Bay: U.S. Geological Survey Open-File Report 80-1297, 68 p.

Cheng, R.T., and Gartner, J.W., 1984, Tides, tidal and residual currents in San Francisco Bay, California: Results of measurements, 1979-1980: U.S. Geological Survey Water Resources Investigations Report 84-4339,
Part I. Description of Data, 72 p,
Part II. Results of measurements in Suisun Bay Region, 231 p,
Part III. Results of measurements in San Pablo Bay Region, 368 p,
Part IV. Results of measurements in central Bay Region, 757 p,
Part V. Results of measurements in south Bay Region, 319 p.

Cheng, R.T., and Gartner, J.W., 1985, Harmonic analysis of tides and tidal currents in south San Francisco Bay, CA: Estuarine, Coastal, and Shelf Science, v. 21, p. 57-74.

Cheng, R.T., Gartner, J.W., Cacchione, D.A., and Tate, G.B., 1998, Flow and suspended particulate transport in a tidal bottom layer, south San Francisco Bay, California, in Dronkers, J., and Scheffers, M.B.A.M., eds., Proceedings from the 8th International Biennial Conference on Physics of Estuaries and Coastal Seas: Rotterdam, Netherlands, A.A. Balkema, p. 3-12.

Cheng, R.T., Gartner, J.W., Cacchione, D.A., and Tate, G.B., 1998, Flow and suspended particulate transport in a tidal bottom layer, south San Francisco Bay, California, in Dronkers, J., and Scheffers, M.B.A.M., eds., Proceedings from the 8th International Biennial Conference on Physics of Estuaries and Coastal Seas: Rotterdam, Netherlands, A.A. Balkema, p. 3-12.

Cheng, R.T., Gartner, J.W., and Smith, R.E., 1997, Bottom boundary layer in south San Francisco Bay, California, 7th International Biennial Conference on Physics of Estuaries and Coastal Seas, Woods Hole Oceanographic Institute, Woods Hole, Mass., November 28-30, 1994: Journal of Coastal Research, v. SI, no. 25, p. 49-62.

Cheng, R.T., Ling, C.H., Gartner, J.W., and Wang, P.F., 1999, Estimates of bottom roughness length and bottom shear stress in south San Francisco Bay, California: Journal of Geophysical Research, v. 104, no. C4, p. 7,715-7,728.

Cheng, Ralph T., McKinnie, D., English, C., and Smith, R.E., 1998,  An Overview of San Francisco Bay PORTS: Ocean Community Conference, Marine Technology Society, Baltimore, November 15-19, 1998, p. 1,054-1,060.

Cheng, R.T., and Smith, L.H., 1986, Tidal hydraulics of San Francisco Bay: Proceedings, Symposium on San Joaquin Valley Agriculture Waste Water and Implications for the San Francisco Bay Estuarine System, p. 130-149.

Cheng, R.T., and Smith, P.E., 1990, A survey of three-dimensional numerical estuarine models, in Spaulding, M., ed, Estuarine and Coastal Modeling: American Society of Civil Engineers Specialty Conference, p. 1-15.

Cheng, R.T., Smith, P.E., and Casulli, V., 1993, Recent development in three-dimensional numerical estuarine models, in National Conference on Hydraulic Engineering, 1993, Proceedings: American Society of Civil Engineers, San Francisco, Calif., July 1993, p. 1,982-1,987.

Cheng, Ralph T., and Smith, R.E., 1998, A nowcast model for tides and tidal currents in San Francisco Bay, California: Ocean Community Conference, Marine Technology Society, Baltimore, November 15-19, 1998, p. 537-543.

Cheng, R.T., and Walters, R., 1981, Some finite element applications in environmental hydrodynamics, in Abel, J., ed., Interdisciplinary Finite Element Analysis: Cornell University College of Engineering, p. 233-365.

Cheng, R.T., and Walters, R.A., 1982, Modeling of estuarine hydrodynamics and field data requirements: Finite Methods in Fluids, v. 4, p. 89-108.

Cheng, R.T., and Wang, L., 1985, Solid state recording current meter conversion: Proceedings, Oceans, v. 85, p. 752-754.

Chin, J.L., Orzech, K., Anima, R.J., and Jaffe, B., 2002, Modern estuarine sedimentation in Suisun Bay, California [abs.]: EOS, American Geophysical Union Transactions, v. 83, no. 47, [abs. OS61A-0204].

Chin, J.L., Wolf, S.C., and Rubin, D.M., 2000, Shallow subbottom stratigraphy and Late Quaternary history, Grizzly and Suisun Bays, California: U.S. Geological Survey Miscellaneous Field Investigations Map, 4-6 color plates at scale 1:20,000 and 1:5,000 with text.

Cifuentes, L.A., Schemel, L.E., and Sharp, J.H., 1990, Qualitative and numerical analyses of the effects of river inflow variations on mixing diagrams in estuaries: Estuarine Coastal and Shelf Science, v. 30, p. 411-427.

CIRMOUNT Committee, 2006, Mapping New Terrain: Climate Change and America’s West. Report of the Consortium for Integrated Climate Research in Western Mountains (CIRMOUNT), Misc Pub., PSW-MISC-77, Albany, CA, Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture, 29pp.

Cloern, J.E., 1976, Recent limnological changes in southern Kootenay Lake, British Columbia: Canadian Journal of Zoology, v. 54, no. 9, p. 1,571-1,578.

Cloern, J.E., 1976, The survival of coho salmon (Oncorhynchus kisutch) eggs in two Wisconsin tributaries of Lake Michigan: The American Midland Naturalist, v. 96, no. 2, p. 451-461.

Cloern, J.E., 1977, Effects of light intensity and temperature on Cryptomonas ovata (Cryptophyceae) growth and nutrient uptake rates: Journal of Phycology, v. 13, p. 389-395.

Cloern, J.E., 1978, Empirical model of Skeletonema costatum photosynthetic rate, with applications in the San Francisco Bay estuary: Advances in Water Resources, v. 1, no. 5, p. 267-274.

Cloern, J.E., 1978, Simulation model of Cryptomonas ovata population dynamics in southern Kootenay Lake, British Columbia: Ecological Modelling, v. 4, p. 133-149.

Cloern, J.E., 1979, Phytoplankton ecology of the San Francisco Bay system - The status of our current understanding, in Conomos, T.J., ed., San Francisco Bay - The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, June 12-16, 1977, p. 247-264.

Cloern, J.E., 1982, Does the benthos control phytoplankton biomass in south San Francisco Bay?: Marine Ecology Progress Series, v. 9, p. 191-202.

Cloern, J.E., 1984, Temporal dynamics and ecological significance of salinity stratification in an estuary (south San Francisco Bay, USA): Oceanologica Acta, v. 7, p. 137-141.

Cloern, J.E., 1987, Turbidity as a control on phytoplankton biomass and productivity in estuaries: Continental Shelf Research, v. 7, p. 1,367-1,381.

Cloern, J.E., 1991, Annual variations in river flow and primary production in the south San Francisco Bay estuary (USA), in Elliot, M., and Ducrotoy, D., eds., Estuaries and Coasts - Spatial and Temporal Intercomparisons: Denmark, Olsen and Olsen Publishers, p. 91-96.

Cloern, J.E., 1991, Tidal stirring and phytoplankton bloom dynamics in an estuary: Journal of Marine Research, v. 49, p. 203-221.

Cloern, J.E., 1995, Ecosystem responses to phytoplankton blooms - Examples from south San Francisco Bay, Interagency Ecological Program for the Sacramento - San Joaquin Estuary Newsletter: California Department of Water Resources, p. 10-13.

Cloern, J.E., 1996, Phytoplankton bloom dynamics in coastal ecosystems: a review with some general lessons from sustained investigation of San Francisco Bay, California: Reviews of Geophysics, v. 34, no. 2, p. 127-168.

Cloern, J.E., 1999, A CALFED-supported study of the Delta’s foodweb base: Interagency Ecological Program Newsletter, v. 12, no. 1, p. 19-20.

Cloern, J.E., 1999, The relative importance of light and nutrient limitation of phytoplankton growth - a simple index of coastal ecosystem sensitivity to nutrient enrichment: Aquatic Ecology, v. 33, no. 1, p. 3-16.

Cloern, J.E., 2001, Our evolving conceptual model of the coastal eutrophication problem: Marine Ecology Progress Series, v. 210, p. 223-253.

Cloern, J.E., 2007, Habitat Connectivity and Ecosystem Productivity: Implications from a Simple Model, The American Naturalist 169:E21-E33.

Cloern, J.E., Alpine, A.E., and Cole, B.E., 1997, Seasonal comparisons of seston abundance and sedimentation rate in a closed-basin lake (Williams) and an open-basin lake (Shingobee): U.S. Geological Survey Water-Resources Investigations Report 96-4215, p. 111-117.

Cloern, J.E., Alpine, A.E., Cole, B.E., and Heller, T., 1992, Seasonal changes in the spatial distribution of phytoplankton in small, temperate-zone lakes: Journal of Plankton Research, v. 14, p. 1,017-1,024.

Cloern, J.E., Alpine, A.E., Cole, B.E., Wong, R.L.J., Arthur, J.F., and Ball, M.D., 1983, River discharge controls phytoplankton dynamics in northern San Francisco Bay estuary: Estuarine Coastal Shelf Science, v. 12, p. 415-429.

Cloern, J.E., Canuel, E.A., and Harris, D., 2002,  Stable carbon and nitrogen isotope composition of aquatic and terrestrial plants of the San Francisco Bay estuarine system.  Limnology and Oceanography 47: 713-729.

Cloern, J.E., Canuel, E.A., and Wienke, S.M., 1993, Particulate organic matter in the San Francisco Bay estuary, California, chemical indicators of its origin and assimilation into the benthic food web: U.S. Geological Survey Open-File Report 93-146, 42 p.

Cloern, J.E., and Cheng, R.T., 1981, Simulation model of Skeletonema costatum population dynamics in northern San Francisco Bay, California: Estuarine, Coastal and Shelf Science, v. 12, p. 83-100.

Cloern, J.E., Cole, B.E., and Edmunds, J.L., 1996, Seasonal fluctuations of water quality in San Francisco Bay during the first three years of the regional monitoring program, 1993-1995: 1995 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances - San Francisco Estuary Institute, p. 31-43.

Cloern, J.E., Cole, B.E., Edmunds, J.L., and Baylosis, J.I., 1997, Water quality variability in San Francisco Bay, Some general lessons from 1996 sampling: 1996 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances - San Francisco Estuary Institute, p. 46-60.

Cloern, J.E., Cole, B.E., Edmunds, J.L., and Baylosis, J.I., 1999, Water-quality variability in San Francisco Bay: general patterns of change during 1997, in 1997 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances: San Francisco Estuary Institute, p. 67-81.

Cloern, J.E., Cole, B.E., Edmunds, J.L., Schraga, T.S., and Arnsberg, A., 2000, Patterns of water-quality variability in San Francisco Bay during the first six years of the regional monitoring program, 1993-1998, in 1998 Annual Report, San Francisco estuary regional monitoring program for trace substances: San Francisco Estuary Institute, 20 p.

Cloern, J.E., Cole, B.E., Wong, R.L.J., and Alpine, A.E., 1985, Temporal dynamics of estuarine phytoplankton: A case study of San Francisco Bay: Hydrobiologia, v. 129, p. 153-176.

Cloern, J.E., Dufford, R., 2005, Phytoplankton community ecology: principles applied in San Francisco Bay. Marine Ecology Progress Series, 285:11-28.

Cloern, J.E., and Jassby, A.D., 1995, Yearly fluctuation of the spring phytoplankton bloom in south San Francisco Bay - An example of ecological variability at the land-sea interface, in Steele, J.H, Powell, T.M., and Levin, S., eds., Ecological Time Series: Chapman Hall, p. 139-149.

Cloern, J.E., Jassby, A.D., Schraga, T.S., and Dallas, K.L., 2006, What is causing the phytoplankton increase in San Francisco Bay? 2006 Pulse of the Estuary. San Francisco Estuary Institute, Oakland.

Cloern, J.E., A.D. Jassby, J.K. Thompson, K.A. Hieb, 2007, A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay, Proceedings of the National Academy of Sciences of the United States of America, 104 (47): 18561-18565.

Cloern, J.E. and Krantz, T., 2006,  Eutrophication, in Encyclopedia of Earth. Eds. J Emmett Duffy. (Washington, D.C.: Environmental Information Coalition, National Council for Science and the Environment).

Cloern, J.E., Luoma, S.N., and Nichols, F.H., 1995, The United States Geological Survey San Francisco Bay program: lessons learned for managing coastal water resources: U.S. Geological Survey, Fact Sheet FS-053-95, 3 p.

Cloern, J.E., and Nichols, F.H., 1978, A von Bertalanffy growth model with a seasonally varying coefficient: Journal of the Fisheries Research Board of Canada, v. 35, no. 11, p. 1,479-1,482.

Cloern, J.E., and Nichols, F.H., eds., 1985, Temporal dynamics of an estuary: San Francisco Bay: Kluwer, Dordrecht, The Netherlands, 237 p.

Cloern, J.E., and Nichols, F.H., 1985, Time scales and mechanisms of estuarine variability, a synthesis from studies of San Francisco Bay: Hydrobiologia, v. 129, p. 229-237.

Cloern, J.E., and Oremland, R.S., 1983, Chemistry and microbiology of a sewage spill in south San Francisco Bay: Estuaries, v. 6, no. 4, p. 399-406.

Cloern, J.E., Powell, T.M., and Huzzey, L.M., 1989, Spatial and temporal variability in south San Francisco Bay, II, Temporal changes in salinity, suspended sediments, and phytoplankton biomass and productivity over tidal time scales: Estuarine, Coastal and Shelf Science, v. 28, p. 599-613.

Cloern, J.E., Schraga, T.S., Lopez, C.B., and Labiosa, R., 2003, Lessons from monitoring water quality in San Francisco Bay, in 2003 Pulse of the Estuary, Monitoring and Managing Contamination in the San Francisco Estuary: San Francisco Estuary Institute, p. 15-20.

Cloern, J.E., Schraga, T.S., and Lopez, C.B., 2005, Heat wave brings a red tide to San Francisco Bay. Eos Transactions of the American Geophysical Union 86(7):66

Cloern, J.E., Schraga, T.S., Lopez, C.B., Knowles, N., Labiosa, R.G., and Dugdale, R., 2005, Climate anomalies generate an exceptional dinoflagellate bloom in San Francisco Bay, Geophysical Research Letters 32, LI4608.

Cole, B., and Cohen, A., 1998, Red tide in Berkeley marina raises concern for toxic blooms in central Bay: Newsletter, Interagency Ecological Program for the Sacramento - San Joaquin Estuary, v. 11, p. 11-13.

Cole, B.E., Cloern, J.E., and Alpine, A.E., 1986, Biomass and productivity of three phytoplankton size classes in San Francisco Bay: Estuaries, v. 9, no. 2, p. 117-126.

Cole, B.E., Cloern, J.E., and Alpine, A.E., 1997, The photosynthetic response of phytoplankton in Shingobee Lake and Williams Lake: U.S. Geological Survey Water-Resources Investigations Report 96-4215, p. 105-110.

Cole, B.E., Hager, S.W., Hollibaugh, J.T., 1990, Hydrographic, biological, and nutrient properties of Tomales Bay, California, March 1985 to May 1986: U.S. Geological Survey Open-File Report 90-178.

Cole, B.E., and Herdon, R.E., 1979, Hydrographic properties and primary productivity of San Francisco Bay waters: U.S. Geological Survey Open-File Report 79-983, 97 p.

Cole, B.E., Thompson, J.K., and Cloern, J.E., 1992, Measurement of filtration rates by infaunal bivalves in a recirculating flume: Marine Biology, v. 113, p. 219-225.

Conomos, T.J., 1975, Movement of spilled oil as predicted by estuarine non-tidal drift: Limnology and Oceanography, v. 20, p. 159-173.

Conomos, T.J., 1979, Properties and circulation of San Francisco Bay waters, in Conomos, T.J., ed., San Francisco Bay – The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, 493 p.

Conomos, T.J., 1979, San Francisco Bay - the urbanized estuary, in Conomos, T.J., ed.: American Association for the Advancement of Science, Pacific Division, San Francisco, 493 p.

Conomos, T.J., and Peterson, D.H., 1974, Biological and chemical aspects of the San Francisco Bay turbidity maximum: Memoires Institute Geologie du Bassind Aquitaine, v. 7, p. 45-52.

Conomos, T.J., and Peterson, D.H., 1975, Longitudinal distribution of selected micro-nutrients in northern San Francisco Bay during 1972, in Brown, R.L., ed., Proceedings, Workshop on Algae Nutrient Relationships in the San Francisco Bay Delta, 8-10 November 1973, Clear Lake, Calif.: S.F. Bay and Estuarine Association, p. 103-126.

Conomos, T.J., and Peterson, D.H., 1977, Suspended particle transport and circulation in San Francisco Bay - An overview, in Wiley, M., ed., Estuarine Processes: Academic Press, New York, p. 82-97.

Conomos, T.J., Nichols, F.H., Cheng, R.T., and Peterson, D.H., 1978, Field and modeling studies of San Francisco Bay, in Symposium on Technical, Environmental, Socio-Economic and Regulatory Aspects of Coastal Zone Management Proceedings: American Society of Civil Engineers, San Francisco, p. 1,917-1,927.

Conomos, T.J., Peterson, D.H., Carlson, P.R., and McCulloch, D.S., 1970, Movement of sea bed drifters in the San Francisco Bay estuary and the adjacent Pacific Ocean: A preliminary report: U.S. Geological Survey Circular 837B, 8 p.

Conomos, T.J., Smith, R.E., and Gartner, J.W., 1985, Environmental setting of San Francisco Bay: Hydrobiologia, v. 129, p. 1-12.

Conomos, T.J., Smith, R.E., Peterson, D.H., Hager, S.W., and Schemel, L.E., 1979, Processes affecting seasonal distribution of water properties in the San Francisco Bay estuarine system, in Conomos, T.J., ed., San Francisco Bay - The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 115-142.

Crepeau, K.L., Domagalski, J.L., and Kuivila, K.M., 1994, Methods of analysis and quality assurance practices of the U.S. Geological Survey organic laboratory, Sacramento, California - determination of pesticides in water by solid-phase extraction and capillary-column gas chromatography mass spectrometry: U.S. Geological Survey Open-File Report 94-362, 17 p.

Crepeau, K.L., Kuivila, K.M., and Domagalski, J.L., 1996, Concentrations of dissolved rice pesticides in the Colusa basin drain and Sacramento River, California, 1990-1992, in Morganwalp, D.W., and Aronson, D.A., eds., Proceedings of the U.S. Geological Survey Toxic Substances Hydrology Program - Technical Meeting, Colorado Springs, Colorado, September 20-24, 1993: U.S. Geological Survey Water-Resources Investigations Report 94-4015, v. 2, p. 711-718.

Crimaldi, J.P., Thompson, J.K., Rosman, J.H., Lowe, R.J., and Koseff, J.R., 2002, Hydrodynamics of larval settlement: the influence of turbulent stress events at potential recruitment sites: Limnology and Oceanography, v. 47, no. 4, p. 1,137-1,151.

Croteau, M., Luoma, S.N., and Stewart, A.R., 2005, Trophic transfer of metals along freshwater food webs: Evidence of cadmium biomagnification in nature, Limnology and Oceanography, v. 50, no.5, p. 1511-1519/

Cuetara, J.I., Burau, J.R., and Schoellhamer, D.H., 2001, Hydrodynamic and Suspended-Solids Concentration Measurements in Suisun Bay, California, 1995; U.S. Geological Survey Open File Report 01-4086.

Culbertson, C.W., Strohmaier, F.E., and Oremland, R.S., 1987, Acetylene as a substrate in the development of primordial bacterial communities: Origins of Life and Evolution of the Biosphere, v. 18, p. 397-407.

Culbertson, C.W., Zehnder, A.J.B., and Oremland, R.S., 1981, Anaerobic oxidation of acetylene by estuarine sediments and enrichment cultures: Applied and Environmental Microbiology, v. 42, p. 396-403.

Dartnell, P., and Gardner, J.V., 1999, Sea-floor images and data from multibeam surveys in San Francisco Bay, southern California, Hawaii, the Gulf of Mexico, and Lake Tahoe, California-Nevada: U.S. Geological Survey Digital Data Series DDS-55 (CD-ROM).

Decho, A.W., and Luoma, S.N., 1991, Time-courses in the retention of food material in the bivalves Potamocorbula amurensis and Macoma balthica significance to the absorption of carbon and chromium: Marine Ecology Progress Series, v. 78, p. 303-314.

Decho, A.W., and Luoma, S.N., 1994, Humic and fulvic acids, sinks or sources in the availability of metals to the marine bivalves Macoma balthica and Potamocorbula amurensis: Marine Ecology Progress Series, v. 108, p. 133-145.

Decho, A.W., and Luoma, S.N., 1996, Flexible digestion strategies and trace metal assimilation in marine bivalves: Limnology and Oceanography, v. 41, p. 568-572.

Dedini, L.A., and Schemel, L.E., 1980, A continuous water-sampling and multi-parameter measurement system for estuaries, an improved system for small vessels: U.S. Geological Survey Open-File Report 80-1293, 49 p.

Dedini, L.A., Schemel, L.E., and Tembruell, M.A., 1981, Salinity and temperature measurements in San Francisco Bay waters, 1980: U.S. Geological Survey Open-File Report 82-125, 130 p.

Dettinger, M.D., 2001, Droughts, epic droughts and droughty centuries - Lessons from a California paleoclimatic record: a PACLIM 2001 meeting report: Interagency Ecological Program Newsletter, v. 14, no. 3, Summer 2001, p. 51-53

Dettinger, M.D., 2001, Floods & droughts: a Sierra Nevada perspective: Proceedings, State of the Estuary Conference, San Francisco, October 9-11 2001, p. 19.

Dettinger, M.D., 2005, A long-term (50 yr) historical perspective on flood-generating winter storms in the American River basin: Proc. 2005 California Extreme Precipitation Symposium, 62-73.

Dettinger, M.D., 2005, From climate-change spaghetti to climate-change distributions for 21_st Century California: San Francisco Estuary and Watershed Science, 3(1), http://repositories.cdlib.org/jmie/sfews/vol3/iss1/art4

Dettinger, M.D., 2006, Fifty-two years of pineapple-express storms across the West Coast of North America: California Energy Commission PIER Energy-Related Environmental Research Report CEC-500-2005-004, 15 p.

Dettinger, M.D., 2006, A component-resampling approach for estimating probability distributions from small forecast ensembles: Climatic Change, 76, 149-168, doi:10.1007/s10584-005-9001-6.

Dettinger, M.D., and Cayan, D.R., 1995, Large-scale atmospheric forcing of recent trends toward early snowmelt runoff in California: Journal of Climate, v. 8, p. 606-623.

Dettinger, M.D., and Cayan, D.R., 2003, Interseasonal covariability of Sierra Nevada streamflow and San Francisco Bay salinity: Journal of Hydrology, v. 277, no. 3/4, p. 164-181.

Dettinger, M.D., Bennett, W.A., Cayan, D.R., Florsheim, J., Hughes, M., Ingram, B.L., Jassby, A., Knowles, N., Malamud, F., Peterson, D.H., Redmond, K., and Smith, L., 2003, Climate science issues and needs of the CALFED Bay-Delta Program: American Meteorological Society, 83rd Annual Meeting, Impacts of Water Availability Symposium, Long Beach, Calif., February 8-13 2003, p. 7.11-1 to 7.11-4.

Dettinger, M.D., Cayan, D.R., and Peterson, D.H., 1995, Sierra Nevada runoff into San Francisco Bay—why has it come earlier recently?: Interagency Ecological Program Newsletter, Summer 1995, p. 1-3.

Dettinger, M.D., Cayan, D.R., and Redmond, K.T., 1999, United States streamflow probabilities based on forecasted La Nina, winter-spring 2000: Experimental Long-Lead Forecast Bulletin, v. 8, no. 4, p. 1-5.

Dettinger, M., Cayan, D., and Redmond, K., 2002, United States streamflow probabilities and uncertainties based on anticipated El Niño, water year 2003: Experimental Long-Lead Forecast Bulletin, v. 11, no. 3, p. 46-52.

Dettinger, M.D., Cayan, D.R., Diaz, H.F., and Meko, D.M., 1998, North-south precipitation patterns in western North America on interannual-to-decadal time scales: Journal of Climate, v. 11, p. 3,095-3,111.

Dettinger, M.D., Cayan, D.R., McCabe, G.J. Jr., and Redmond, K.T., 2000, Winter-spring 2001 United States streamflow probabilities based on anticipated neutral ENSO conditions and recent NPO status: Experimental Long-Lead Forecast Bulletin, v. 9, no. 3, p. 55-60.

Dettinger, M.D., Cayan, D.R., Meyer, M.K., and Jeton, A.E., 2004, Simulated hydrologic responses to climate variations and change in the Merced, Carson, and American River basins, Sierra Nevada, California, 1900-2099: Climatic Change, v. 62, 34 p.

Dettinger, M.D., and Earman, S., 2007, Western ground water and climate change—Pivotal to supply sustainability or vulnerable in its own right?: Association of Ground Water Scientists and Engineers Newsletter, June 2007, 4-5.

Dettinger, M.D., Mo, K., Cayan, D.R., and Jeton, A.E., 1999, Global to local scale simulations of streamflow in the Merced, American, and Carson Rivers, Sierra Nevada, California: Preprints, American Meteorological Society's 14th Conference on Hydrology, Dallas, Tex., January 1999, p. 80-82.

Dettinger, M.D., Peterson, D.H., Diaz, H.F., and Cayan, D.R., 1997, Forecasting spring runoff pulses from the Sierra Nevada: Interagency Ecological Program Newsletter, v. 10, no. 3, Summer 1997, p. 32-35.

Dettinger, M.D., Redmond, K.T., and Cayan, D.R., 2004, Winter orographic-precipitation ratios in the Sierra Nevada Large-scale atmospheric circulations and hydrologic consequences: J. Hydrometeorology, 5, 1102-1116.

DiLeo, J., and others, 2003, Notebook of hydroclimatology sites/activities: Yosemite national park: U.S. Geological Survey General Interest Publication, 40 p.

DiLeo, J., Butler, M., Cayan, D., Clow, D., Dettinger, M., Gehvke, F., Hager, S., Lundquist, J., McCurdy, G., Peterson, D., Redmond, K., Riddle, L., Smith, R., and Van Wagtendonk, J., 2004, A Notebook of Hydroclimatology Sites/Activities, Yosemite National Park, U.S. Geological Survey Open-File Report, 39 p.

Dinehart, R.L., and Schoellhamer, D.H., 1999, Sedimentation in the Delta of the Sacramento and San Joaquin Rivers, Proceedings, 4th biennial State of the Estuary Conference, San Francisco, Calif., March 17-19, 1999, p. 75.

Domagalski, J.L., and Kuivila, K.M., 1991, Transport and transformation of dissolved rice pesticides in the Sacramento River Delta, California, in Mallard, G.E., and Aronson, D.A., eds., Proceedings: U.S. Geological Survey Toxic Substances Hydrology Program, Technical Meeting, Monterey, Calif., March 11-15, 1991, p. 664-666.

Domagalski, J.L., and Kuivila, K.M., 1993, Distributions of pesticides and organic contaminants between water and suspended sediment, San Francisco Bay, California: Estuaries, v. 16, no. 3A, p. 416-426.

Downing, B., Wheeler, G., Emerson, S., Ganju, N., and Bergamaschi, B., 2003, Continuous, real-time optical measurement of DOC fluxes in a tidal wetland: Proceedings of the 6th biennial State-of-the-Estuary Conference, Oakland, California, October 21-23, 2003, p. 73.

Duda, T.F., Jr., 1994, Genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay: Marine Biology, v. 119, p. 235-241.

Edmunds, J.L., Cole, B.E., Cloern, J.E., and Dufford, R.G., 1997, Studies of the San Francisco Bay, California, estuarine ecosystem  - pilot regional monitoring program results, 1995: U.S. Geological Survey Open-File Report 97-15, 380 p.

Edmunds, J.L., Cole, B.E., Cloern, J.E., Caffrey, J.M., and Jassby, A.D., 1995, Studies of the San Francisco Bay, California, estuarine ecosystem pilot regional monitoring program results, 1994: U.S. Geological Survey Open-File Report 95-378, 436 p.

Edmunds, J.L., Kuivila, K.M., Cole, B.E., and Cloern, J.E., 1999, Do herbicides impair phytoplankton primary production in the Sacramento - San Joaquin River Delta? in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program - Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2 - Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 81-88.

English, C.A., Gartner, J.W., Smith, R.E., and Cheng, R.T., 1999, A marine now cast system for San Francisco Bay, California, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program - Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2 - Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 65-68.

Feng, S., Cheng, R.T., and Xi, P., 1986, On tide-induced Lagrangian residual current and residual transport, 1, Lagrangian residual current: Water Resources Research, v. 22, p. 1,623-1,634.

Feng, S., Cheng, R.T., and Xi, P., 1986, On tide-induced Lagrangian residual current and residual transport, 2, Residual transport with application in south San Francisco Bay, California: Water Resources Research, v. 22, p. 1,635-1,646.

Field, M.E., Gardner, J.V., Bader, L.R., and Barber, J.H., Jr., 1994, Marine geology expedition to San Francisco Bay: U.S. Geological Survey Open-File Report 94-14, 21 p.

Ford, M., Wang, J., and Cheng, R.T., 1990, Predicting the vertical structure of tidal current and salinity in San Francisco Bay, California: Water Resources Research, v. 26, p. 1,027-1,043.

Fleck, J.A., Bergamaschi, B.A., Downing, B.D., Lionberger, M.A., Schoellhamer, D.H., Boss, E., and Stephenson, M., 2006, A tool for assessing mercury loadings from restored tidal systems: Proceedings of the South Bay Science Symposium, June 6, 2006, San Jose, California, p. 9. Schoellhamer, D.H., Orlando, J.L., Wright, S.A., and Freeman, L.A., 2006, Sediment supply and demand: Proceedings of the South Bay Science Symposium, June 6, 2006, San Jose, California, p. 3.

Florsheim, J., and Dettinger, M., 2005, Influence of anthropogenic alterations on geomorphic response to climate variations and change in San Francisco Bay-Delta and watershed: Watershed Management Council Networker, 13, Spring 2005, 13-16.

Foxgrover, A.C., Higgins, S.A., Ingraca, M.K., Jaffe, B.E., Smith, R.E., 2003, Sedimentation and bathymetry changes in south San Francisco Bay: 1858-1983 [abs.]: 6th Biennial State of the Estuary Conference, Oakland, Calif., October 21-23, 2003, p. 80.

Foxgrover, A.C., Higgins, S.A., Ingraca, M.K., Jaffe, B.E., and Smith, R.E., 2004, Deposition, erosion, and bathymetric change in south San Francisco Bay: 1858-1983: U.S. Geological Survey Open-File Report 2004-1192, 25 p.

Foxgrover, A.C. and Jaffe, B.E., 2005, South San Francisco Bay 2004 topographic lidar survey: Data overview and preliminary quality assessment, U.S. Geological Survey Open-File Report OFR-2005-1284, 57 p.

Foxgrover, A.C., Jaffe, B.E., Hovis, G.T., Martin, C.A., Hubbard, J.R., Samant, M.R., and Sullivan, S.M., 2007, 2005 Hydrographic Survey of South San Francisco Bay, California, U.S. Geological Survey Open-File Report 2007-1169, 113 p. [URL: http://pubs.usgs.gov/of/2007/1169].

Foxgrover, A.C. and Jaffe, B.E., 2006, Historic bathymetric surveys provide valuable information for restoration planning: South San Francisco Bay, CA, (abs) Restore Americas Estuaries Conference, New Orleans, LA.

Foxgrover, A. C., and Jaffe, B. E., 2006, Historic Bathymetric Change in South San Francisco Bay: is There Enough Sediment Available to Restore the Salt Ponds?: (abs.) Fourth Biennial CALFED Science Conference.

Fregoso, T., Jaffe, B.E., Rathwell, G., Collins, W., Rhynas, K., Sullivan, S., Tomlin, V., Thompson, J., and Parchaso, F., 2006, Mapping South San Francisco Bay's seabed diversity for use in wetland restoration planning, (abs) Restore Americas Estuaries Conference, New Orleans, LA.

Fujii. R., Bergamaschi, B.A., Ganju, N.K., Fleck, J.A., Burow-Fogg, K.R., Schoellhamer, D., Deverel, S.J., 2003, Preliminary Assessment of DOC and THM Precursor Loads from a Freshwater Restored Wetland, an Agricultural Field, and a Tidal Wetland in the Sacramento-San Joaquin River Delta: Proceedings of the 2003 CALFED Science Conference, Sacramento, California, January 14-16, 2003, p. 206.

Fuller, C.C., and Hammond, D.E., 1983, The fallout rate of Pb-210 on the western coast of the United States: Geophysical Research Letters, v. 10, p. 1,164-1,167.

Fuller, C.C., van Geen, A. Baskaran, M., and Anima, R., 1999, Sediment chronology in San Francisco Bay, California, defined by 210Pb, 234Th, 137Cs, and 239,240Pu: Marine Chemistry, v. 64, nos. 1 & 2, p. 7-27.

Ganju, N.K. and Schoellhamer, D.H., 2003, Tidal and vertical variability of floc characteristics: Proceedings of the 7th International Conference on Nearshore and Estuarine Cohesive Sediment Transport Processes: Gloucester Point, Virginia, October 1-4, 2003, p. 6.

Ganju, N.K., and Schoellhamer, D.H., 2006, Annual sediment flux estimates in a tidal strait using surrogate measurements: Estuarine, Coastal and Shelf Science, v. 69, p. 165-178.

Ganju, N.K., Bergamaschi, B., and Schoellhamer, D.H., 2003, Tidal wetland fluxes of dissolved organic carbon and sediment at Browns Island, California: Initial evaluation: Proceedings of the 2003 CALFED Science Conference, Sacramento, California, January 14-16, 2003, p. 208.

Ganju, N.K., Schoellhamer, D.H., and Bergamaschi, B.A., 2005, Suspended sediment fluxes in a tidal wetland: measurement, controlling factors, and error analysis: Estuaries, v. 28, no. 6, p. 812-822.

Ganju, N.K., Schoellhamer, D.H., Murrell, M.C., Gartner, J.W., and Wright, S.A., 2007, Constancy of the relation between floc size and density in San Francisco Bay, in Maa, J.P.-Y., Sanford, L.P., and Schoellhamer, D.H., ed., Estuarine and Coastal Fine Sediments Dynamics: Elsevier Science B.V., p. 75-91.

Ganju, N.K., Schoellhamer, D.H., Warner, J.C., Barad, M.F., and Schladow, S.G., 2004, Tidal oscillation of sediment between a river and a bay: a conceptual model: Estuarine, Coastal and Shelf Science, v. 60, no. 1, p. 81-90.

Gartner, J.W., 1986, Tides and residual currents near the confluence of the Sacramento and San Joaquin Rivers, results of measurements, 1984-85: U.S. Geological Survey Water Resources Investigations Report 86-4025, 42 p.

Gartner, J.W., and Burau, J.R., 1999, Hydrodynamic measurements in Suisun Bay, California, 1992-1993: U.S. Geological Survey Water Resources Investigation Report 99-4039, 179 p.

Gartner, J.W., and Cheng, R.T., 1982, Observations from moored current meters in San Francisco Bay: U.S. Geological Survey Open-File Report 82-153, 91 p.

Gartner, J.W., and Cheng, R.T., 1983, Observations from remote weather stations in San Francisco Bay, California, 1979-1981: U.S. Geological Survey Open-File Report 83-269, 120 p.

Gartner, J.W., and Cheng, R.T., 1987, Propogation of tides in south, central and San Pablo Bays, California - Comparison of model results and field observations: Proceedings, Workshop on Hydrodynamics of San Francisco Bay/Delta, Sausalito, Calif., May 22-23, 1987.

Gartner, J.W., and Cheng, R.T., 1996, Near bottom velocity measurements in San Francisco Bay, California: Proceedings, Oceans 1996 Marine Technology Society Marine Technology Society/Institute of Electrical and Electronics Engineers Conference, Fort Lauderdale, Fla., Sept. 23-26, 1996, p. 457-462.

Gartner, J.W., Cheng, R.T., Cacchione, D.A., and Tate, G.B., 1997, Near bottom velocity and suspended solids measurements in San Francisco Bay, California: Proceedings, 27th Congress of the International Association for Hydraulic Research, American Society of Civil Engineers, San Francisco, Calif., August 1997, p. 1,090-1,095.

Gartner, J.W., and Oltmann, R.N., 1985, Comparison of recording current meters used for measuring velocities in shallow waters of San Francisco Bay, California, v. 2 of Ocean Engineering and the Environment, San Diego, California, November 12-14, Oceans 1985 Conference Record: Washington, D.C., Marine Technology Society, p. 731-737.

Gartner, J.W., and Oltmann, R.N., 1990, Comparison of recording current meters in shallow water of San Francisco Bay, California: U.S. Geological Survey Water Resources Investigations Report, 90-4018, 84 p.

Gartner, J.W., and Walters, R.A., 1986, Tidal and residual currents in south San Francisco Bay, California, results of measurements in, 1981-1983: U.S. Geological Survey Water Resources Investigations Report 86-4024, 148 p.

Gartner, J.W., and Yost, B.T., 1988, Tides and tidal and residual currents in San Pablo and Suisun Bays, California—Results of Measurements, 1986: U.S. Geological Survey Water Resources Investigations Report 88-4027, 94 p.

Grenz C., Cloern, J.E., Hager, S.W., and Cole, B.E., 2000, Dynamics of nutrient cycling and related benthic nutrient and oxygen fluxes during a spring phytoplankton bloom in south San Francisco Bay (USA): Marine Ecology Progress Series, v. 197, p. 67-80.

Griscom, S.B., Fisher, N.S., and Luoma, S.N., 2000, Geochemical influences on assimilation of sediment-bound metals in clams and mussels: Environmental Science & Technology, v. 34, no. 1, p. 91-99.

Guarini, J.M., Cloern, J.E., Edmunds, J., Gros, P., 2002, Microphytobenthos potential productivity estimated in three tidal embayments of the San Francisco Bay system: Estuaries, v. 25, p. 409-417.

Hager, S.W., 1993, Dissolved nutrient and suspended particulate matter data for the San Francisco Bay estuary, California, October 1988 through September 1991: U.S. Geological Survey Open-File Report 93-57, 51 p.

Hager, S.W., 1994, Dissolved nutriissolved nutrient and suspended particulate matter data for the San Francisco Bay estuary, California, October 1991 through November 1993: U.S. Geological Survey Open-File Report 94-471, 53 p.

Hager, S.W., 1994, Particulate carbon and nitrogen and suspended particulate matter in the Sacramento River at Rio Vista, California, January 3 – May 26, 1983 and October 31, 1983 – November 29, 1984: U.S. Geological Survey Open-File Report 94-470, 35 p.

Hager, S.W., and Harmon, D.D., 1984, Chemical determination of particulate nitrogen in San Francisco Bay, a comparison of two estimates: Estuarine, Coastal and Shelf Science, v. 19, p. 181-191.

Hager, S.W., and Schemel, L.E., 1992, Sources of nitrogen and phosphorus to northern San Francisco Bay: Estuaries, v. 15, no. 1, p 40-52.

Hager, S.W., and Schemel, L.E., 1996, Dissolved inorganic nitrogen, phosphorus, and silicon in south San Francisco Bay, I, major factors affecting distributions, in Hollibaugh, J.T., ed., San Francisco Bay – The Ecosystem: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 189-215.

Hager, S.W. and Schemel, L.E., 1997, Effects of reduced wastewater phosphate concentrations in South San Francisco Bay: Interagency Ecological Program Newsletter, v.10, n.3, p.11-12.

Hager, S.W., and Schemel, L.E., 1997, Dissolved nutrient data for the San Francisco Bay estuary, California, January through November 1995: U.S. Geological Survey Open-File Report 97-359.

Hager, S.W., Cole, B.E., and Schemel, L.E., 1979, Phytoplankton productivity measurement in San Francisco Bay estuary, a comparison of four methods: U.S. Geological Survey Open-File Report 80-766, 32 p.

Hager, S.W., Harmon, D.D., and Alpine, A.E., 1984, Chemical determination of particulate nitrogen in San Francisco Bay, nitrogen: chlorophyll–a ratios in plankton: Estuarine, Coastal and Shelf Science, v. 19, p. 193-204.

Hammond, D.E., and Fuller, C., 1979, The use of Radon-222 to estimate benthic exchange and atmospheric exchange rates in San Francisco Bay, in Conomos, T.J., ed., San Francisco Bay – The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 213-230.

Hammond, D.E., Fuller, C., Harmon, D., Hartman, B., Korosec, M., Miller, L.G., Rea, R., Warren, S., Berelson, W., and Hager, S.W., 1985, Benthic fluxes in San Francisco Bay: Hydrobiologia, v. 129, p. 69-90.

Hampton, M.A., Snyder, N.P., Chin, J.L., Allison, D.W., and Rubin, D.M., 2003, Bed-sediment grain-size and morphologic data from Suisun, Grizzly, and Honker Bays, Calif., 1998-2002: U.S. Geological Survey Open-File Report 2003-250, 25 p.

Hanson, R.T., Dettinger, M.D., and Newhouse, M.W., 2006, Relations between climatic variability and hydrologic time series from four alluvial basins across the southwestern United States: Hydrogeology Journal, doi:10.1007/s10040-006-0067-7, 25 p.

Harmon, D.D., Schemel, L.E., Hager, S.W., and Ota, A.Y., 1986, Physical and chemical data for the Sacramento River at Rio Vista, California, January through May, 1983: U.S. Geological Survey Open-File Report 86-230, 26 p.

Hartman, B., and Hammond, D.E., 1984, Gas exchange rates across the sediment-water and air-water interfaces in south San Francisco Bay: J. Geophysical Research, v. 89, p. 3,593-3,603.

Harvey, R.W., and Luoma, S.N., 1984, The role of bacterial exopolymer and suspended bacteria in the nutrition of the deposit-feeding clam, Macoma balthica: Journal of Marine Research, v. 42, p. 957-968.

Harvey, R.W., and Luoma, S.N., 1985, Effect of adherent bacteria and bacterial extra cellular polymers upon assimilation by Macoma balthica of sediment-bound Cd, Zn and Ag: Marine Ecology-Progress Series, v. 22, p. 281-289.

Harvey, R.W., and Luoma, S.N., 1985, Separation of solute and particulate vectors of heavy metal uptake in controlled suspension-feeding experiments with Macoma balthica: Hydrobiologia, v. 121, p. 97-102.

Harvey, R.W., Lion, L.W., and Young, L.Y., 1983, Transport and distribution of bacteria and diatoms in the aqueous surface micro-layer of a salt marsh: Estuarine, Coastal and Shelf Science, v. 16, p. 543-547.

Harvey, R.W., Lion, L.W., Young, L.Y., and Leckie, J.O., 1982, Enrichment and association of lead and bacteria at particulate surfaces in a salt marsh surface layer: Journal of Marine Research, v. 49, no. 4, p. 1,201-1,211.

Higgins, S.A., Smith, R.E., Fuller, C.C., and Jaffe, B.E., 2003, A model for reconstructing the history of sediment deposition in San Pablo Bay Between 1856 and 1983 [abs.]: 6th Biennial State of the Estuary Conference, Oakland, Calif., October 21-23, 2003, p. 88.

Higgins, S.A., Jaffe, B.E., and Smith, R.E., 2005, Bathychronology: Reconstructing historical sedimentation from bathymetric data in a GIS, U.S. Geological Survey Open-File Report OFR-2005-1284, 19 p. plus appendix [URL: http://pubs.usgs.gov/of/2005/1273/].

Higgins, S.A., Jaffe, B.E., and Fuller, C.C., 2007, Reconstructing sediment age profiles from historical bathymetry changes in San Pablo Bay, California, Estuarine Coastal and Shelf Science, doi:10.1016/j.ecss.2006.12.018.

Hopkins, D.R., 1986, Atlas of the distributions and abundances of common benthic species in San Francisco Bay, California: U.S. Geological Survey Water Resources Investigations Report 86-4003, 228 p.

Hopkins, D.R., 1987, Temporal variations in the benthic communities at four intertidal sites in San Francisco Bay, California, 1983-85: U.S. Geological Survey Open-File Report 87-387, 89 p.

Hornberger, M.I., Luoma, S.N., Cain, D.J., Parchaso, F., Brown, C.L., Bouse, R.M., Wellise, C., and Thompson, J., 1999, Bioaccumulation of metals by the bivalve Macoma balthica at a site in south San Francisco Bay between 1977 and 1997: Long-term trends and associated biological effects with changing pollutant loadings: U.S. Geological Survey, Open-File Report 99-55, 42 p.

Hornberger, M.I., Luoma, S.N., Cain, D.J., Parchaso, F., Brown, C.L., Bouse, R.M., Wellise, C., and Thompson, J.K, 2000, Linkage of bioaccumulation and biological effects to changes in pollutant loads in south San Francisco Bay: Environmental Science and Technology, v. 34, no. 12, p. 2,401-2,409.

Hornberger, M.I., Luoma, S.N., van Geen, A., Fuller, C., and Anima, R., 1999, Historical trends of metals in the sediments of San Francisco Bay, California: Marine Chemistry, v. 64, p. 39-55.

Hostettler, F.D., Pereira, Wilfred E., Kvenvolden, K.A., Jones, D.R., and Murphy, F., 1996, Preliminary geochemical studies of pollutant and natural organic compounds in sediments from Sonoma Baylands -- a wetland restoration project in San Francisco Bay, California: U.S. Department of the Interior/U.S. Geological Survey, Open-File Report 96-48.

Hostettler, F.D., Pereira, W.E., Kvenvolden, K.A., Jones, D.R., and Murphy, F., 1997, Reclamation of bay wetlands and disposal of dredge spoils – meeting two goals simultaneously: U.S. Geological Survey Fact Sheet FS-042-97.

Hostettler, F.D., Pereira, W.E., Kvenvolden, K.A., van Geen, A., Luoma, S.N., Fuller, C.C., and Anima, R.J., 1999, A record of hydrocarbon input to San Francisco Bay as traced by biomarker profiles in surface sediment and sediment cores: Marine Chemistry, v. 64, p. 115-127.

Hostettler, F.D., Rapp, J.B., and Kvenvolden, K.A., 1991, Use of geochemical biomarkers in bottom sediment to track oil from a spill, San Francisco Bay, California: Marine Pollution Bulletin, v. 24, p. 15-20.

Hostettler, F.D., Rapp, J.B., Kvenvolden, K.A., and Luoma, S.N., 1989, Biogenic and anthropogenic organic markers as source discriminants and sediment transport indicators in south San Francisco Bay, California: Geochimica Cosmochimica Acta, v. 53, p. 1,563-1,576.

Hostettler, F.D., Rapp, J.B., Pereira, W.E., and Kvenvolden, K.A., 1996, A survey of molecular marker compounds in sediments of San Francisco Bay, California: in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program, Proceedings of the Technical Meeting, Colorado Springs, Colo., September 20-24, 1993: U.S. Geological Survey Water-Resources Investigations Report 94-4105, v. 2, p. 735-746.

Howarth, R., Anderson, D., Cloern, J., Elfring, C., Hopkinson, C., Lapointe, B., Malone, T., Marcus, N., McGlathery, K., Sharpley, A., and Walker, D., 2000, Nutrient pollution of coastal rivers, bays, and seas: Issues in Ecology, no. 7, p. 1-15.

Hunter, Y.R., and Kuwabara, J.S., 1993, Ionic strength and DOC determinations from various freshwater sources to the San Francisco Bay: Bulletin of Environmental Contamination and Toxicology, v. 52, no. 2, p. 311-318.

Hutchins, D.A., Stupakoff, I., Hook, S., Luoma, S.N., and Fisher, N.S., 1998, Effects of arctic temperatures on distribution and retention of the nuclear waste radionuclides ²⁴¹Am, ⁵⁷Co, and ¹³⁷Cs in the bioindicator bivalve Macoma balthica: Marine Environmental Research, v. 45, p. 17-29.

Hutchinson, A., 1981, Plankton studies in San Francisco Bay, III, zooplankton species composition and abundance in the south Bay, 1978-1979: U.S. Geological Survey Open-File Report 81-132, 107 p.

Hutchinson, A., 1982, Plankton studies in San Francisco Bay, V, Zooplankton species composition and abundance in the south Bay, 1980-1981: U.S. Geological Survey Open-File Report 82-1002, 135 p.

Hutchinson, A., 1982, Plankton studies in San Francisco Bay, VI, Zooplankton species composition and abundance in the north bay, 1979-1980: U.S. Geological Survey Open-File Report 82-1003, 185 p.

Huzzey, L.M., Cloern, J.E., and Powell, T.M., 1990, Episodic changes in lateral transport and phytoplankton distribution in south San Francisco Bay: American Society of Limnology and Oceanography, v. 35, no. 2, p. 472-478.

Iversen, N., Oremland, R.S., and Klug, M.J., 1987, Big Soda Lake (Nevada), 3, Pelagic methanogenesis and anaerobic methane oxidation: American Society of Limnology and Oceanography, v. 32, no. 4, p. 804-814.

Jaffe, B.E., 2001, Mercury-contaminated sediments in the north bay–a legacy of the Gold Rush: northern California Geological Society Newsletter, June 2001.

Jaffe, B.E., 2006, The role of sediment supply in intertidal mudflat change in San Pablo Bay, California, (abs) Physics of Estuaries and Coastal Seas Conference, Astoria, OR.

Jaffe, B.E. and Foxgrover, A.C., 2006a, Sediment Deposition and Erosion in South San Francisco Bay, California from 1956 to 2005: U.S. Geological Survey Open-File Report 2006-1287, 24 p.

Jaffe, B.E. and Foxgrover, A.C., 2006b, A history of tidal flat area in South San Francisco Bay, California, from 1858 to 2005: U.S Geological Survey Open File Report 2006-1262, 28 p.

Jaffe, B.E., Smith, R.E., and Torresan, L., 1998, Sedimentation and bathymetric change in San Pablo Bay, 1856-1983: U.S. Geological Survey Open-File Report 98-759.

Jaffe, B.E., Smith, R.E., Bouse, R., and Luoma, S., 2001, Sedimentation, erosion, and mercury contamination: the story of hydraulic gold mining debris in north San Francisco Bay [abs.]: 5th Biennial State of the Estuary Conference, San Francisco, Calif., October, p. 31.

Jaffe, B.E., Smith, R.E., and Foxgrover, A.C., 2007. Anthropogenic influence on sedimentation and intertidal mudflat change in San Pablo Bay, California: 1856 to 1893. Estuarine, Coastal and Shelf Science 73 (1-2), 175-187, doi:10.1016/j.ecss.2006.12.017.

Jassby, A.D., and Cloern, J.E., 2000, Organic matter sources and rehabilitation of the Sacramento-San Joaquin Delta (California, USA): Aquatic Conservation: Marine and Freshwater Ecosystems, p. 323-352.

Jassby, A.D., Cloern, J.E., and Cole, B.E., 2002, Annual primary production: patterns and mechanisms of change in a nutrient-rich tidal ecosystem: Limnology and Oceanography, v. 47, p. 698-712.

Jassby, A.D., Cloern, J.E., and Mueller-Solger, A., 2003, Phytoplankton fuels the food web in Delta waterways: California Agriculture, v. 57, p. 104-109.

Jassby, A.D., Cloern, J.E., and Powell, T.M., 1993, Organic carbon sources and sinks in San Francisco Bay: variability induced by river flow: Marine Ecology Progress Series, v. 95, p. 39-54.

Jassby, A.D., Cloern, J.E., Caffrey, J., Cole, B., and Rudek, J., 1994, San Francisco Bay/delta regional monitoring program plankton and water quality pilot study, 1993, in 1993 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances: San Francisco Estuary Institute, p. 117-128.

Jassby, A.D., Cloern, J.E., Cole, B.E., and Caffrey, J.M., 1995, Choosing optimum station configurations for summarizing water quality characteristics, in 1994 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances: San Francisco Estuary Institute, p. 185-197.

Jassby, A.D., Cole, B.E., and Cloern, J.E., 1997, The design of sampling transects for characterizing water quality in estuaries: Estuarine, Coastal and Shelf Science, v. 45, p. 285-302.

Jassby, A.D., Kimmerer, W.J., Monismith, S.G., Armor, C., Cloern, J.E., Powell, T.M., Schubel, J.R., and Vendlinski, T., 1995, Isohaline position as a habitat indicator for estuarine populations: Ecological Applications, v. 5, no. 1, p. 272-289.

Jennings, B., Schoellhamer, D.H., and Kuivila, K.M., 1997, Optimum sampling strategy for sediment-associated pesticides in Suisun Bay: Interagency Ecological Program Newsletter, v. 10, no. 4, p. 16-20.

Johansson, C., Cain, D.J., and Luoma, S.N., 1986, Variability in the fractionation of Cu, Ag, and Zn among cytosolic proteins in the bivalve Macoma balthica, Marine Ecology Progress Series, v. 28, p. 87-97.

Johns, C., and Luoma, S.N., 1990, Arsenic in benthic bivalves of San Francisco Bay and Sacramento/San Joaquin River Delta: Science of the Total Environment, v. 97/98, p. 673-684.

Johns, C., Luoma, S.N., and Elrod, V., 1988, Selenium accumulation in benthic bivalves and fine sediments of San Francisco Bay, the Sacramento-San Joaquin Delta, and selected tributaries: Estuarine, Coastal and Shelf Science, v. 27, p. 381-396.

Jones, C. and Jaffe, B.E., 2006, Sediment stability measurements, modeling, and long-term sediment transport processes in San Francisco Bay, (abs) Physics of Estuaries and Coastal Seas Conference, Astoria, OR.

Jones, N.W., Monismith, S.G., and Thompson, J.K., 2005, Preliminary results from a shallow water benthic grazing study, Interagency Ecological Program Newsletter, 18(1): 7-14.

Khorram, S.G., Catts, P., Cloern, J.E., and Knight, A.W., 1987, Modeling of estuarine chlorophyll a from an airborne scanner: Institute for Electrical and Electronic Engineers Transactions on Geoscience and Remote Sensing, v. GE-25, no. 6, p. 662-669.

Kiene, R.P., Oremland, R.S., Catena, A., Miller, L.G., and Capone, D.G., 1986, Metabolism of reduced methylated sulfur compounds in anaerobic sediments and by a pure culture of an estuarine methanogen: Applied and Environmental Microbiology, v. 52, p. 1,037-1,045.

Kimmerer, W.J., Burau, J.R., and Bennett, W.A., 1998, Tidally oriented vertical migration and position maintenance of zooplankton in a temperate estuary: Limnology and Oceanography, v. 43, p. 1,697-1,709

Knowles, N., 2000: Modeling the hydroclimate of the San Francisco Bay Delta estuary and watershed: University of California, San Diego, Ph.D. dissertation, 308 p.

Knowles, N., 2000, Natural and human influences on freshwater flows and salinity in the San Francisco Bay delta estuary and watershed: Interagency Ecological Program Newsletter, v. 13, no. 1, p. 15-23.

Knowles, N., 2002, Natural and human influences on freshwater inflows and salinity in the San Francisco estuary at monthly to interannual scales: Water Resources Research, v. 38, no. 12, p. 25.1-25.11.

Knowles, N., and Cayan, D., 2002, Potential effects of global warming on the Sacramento San Joaquin watershed and the San Francisco estuary: Geophysical Research Letters, v. 29, p. 38.1-38.4.

Knowles, N., and Cayan, D., 2004, Elevational dependence of projected hydrologic changes in the San Francisco estuary and watershed: Climatic Change, v. 62, p. 319-336.

Knowles, N., Cayan, D.R., and Peterson, D.H., 1998, Simulated effects of delta outflow on the bay - 1998 compared to other years: Interagency Ecological Program Newsletter, v. 11, no. 4, p. 29-32.

Knowles, N., Cayan, D., Peterson, D.H., Uncles, R.J., 1995, Modeling and predicting intertidal variations of the salinity field in the bay/delta: Interagency Ecological Program Newsletter, v. 8, fall, p. 8-10.

Knowles, N., Cayan, D., Uncles, R., Ingram, L., and Peterson, D., 1997, Diagnosing the flood of 1997 in San Francisco Bay with observations and model results: Interagency Ecological Program for the Sacramento San Joaquin Newsletter, v. 10, no. 3, p. 29-31.

Knowles, N., Peterson, D.H., Uncles, R.J., and Cayan, D.R., 1995, Modeling and predicting intertidal variations in bay/delta: Interagency Ecology Newsletter (DWR), p. 8-10.

Knowles, N., Dettinger, M., and Cayan, D., 2006, Trends in snowfall versus rainfall for the Western United States: Journal of Climate, 19(18), 4545-4559.

Kockelman, W.J., Conomos, T.J., and Leviton, A.E., 1982, San Francisco Bay – use and protection: American Association for the Advancement of Science, Pacific Division, San Francisco, 310 p.

Koczot, K.M., and Dettinger, M.D., 2003, Climate effects of pacific decadal oscillation on streamflow of the Feather River, California: Proceedings, Western Snow Conference, Scottsdale, Ariz., April 21-25, 2003, 4 p.

Koseff, J.R., Holen, J.K., Monismith, S.G., and Cloern, J.E., 1993, Coupled effects of vertical mixing and benthic grazing on phytoplankton populations in shallow, turbid estuaries: Journal of Marine Research, v. 51, no. 4, p. 843-868.

Kuivila, K.M., 1993, Diazinon concentrations in the Sacramento and San Joaquin Rivers and San Francisco Bay, California, February 1993: U.S. Geological Survey Open-File Report 93-440, 2 p. (Water Fact Sheet)

Kuivila, K.M., 1999, Studies relating pesticide concentrations to potential effects on aquatic organisms in the San Francisco Bay Estuary, California, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2—Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 11-16.

Kuivila, K.M., and Copeland, D.D., 1996, Diazinon concentrations and transport in the Sacramento River and San Francisco Bay, California, February, 1993, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Colorado Springs, Colo., September 20-24, 1993: U.S. Geological Survey Water Resources Investigations Report 94-4015, p. 699-704.

Kuivila, K.M., and Foe, C.G., 1995, Concentrations, transport, and biological effects of dormant spray pesticides in the San Francisco Estuary, California: Environmental Toxicology and Chemistry, v. 14, no. 7, p. 1,141-1,150.

Kuivila, K.M. and Moon, G.E., 2004, Potential Exposure of Larval and Juvenile Delta Smelt to Dissolved Pesticides in the Sacramento–San Joaquin Delta, California, in F. Feyrer, L. R. Brown, R. L. Brown, and J. J. Orsi, eds. Early life history of fishes in the San Francisco estuary and watershed. American Fisheries Society Symposium v. 39, p. 229-241.

Kuivila, K.M., and Nichols, F.H., 1991, Overview of San Francisco Bay estuary toxic contaminants study, in Mallard, G.E., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Monterey, Calif., March 11-15, 1991, p. 659-663.

Kuivila, K.M., Barnett, H.D., and Edmunds, J.L., 1999, Herbicide concentrations in the Sacramento–San Joaquin River Delta, California, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2—Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 69-80.

Kuivila, K.M., Sheipline, R.C., and Foe, C.G., 1996, Distribution and possible biological effects of diazinon in the San Joaquin River and the Sacramento–San Joaquin Delta, California, February, 1993, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Colorado Springs, Colo., September 20-24, 1993: U.S. Geological Survey Water Resources Investigations Report 94-4015, p. 705-710.

Kuwabara, J.S., and Baker, J.E., 1993, Trace contaminants and nutrients in estuaries: The importance of process interdependence: Estuaries, v. 16, no. 3A, p. 383-384.

Kuwabara, J.S., Chang, C.C.Y., Cloern, J.E., Fries, T.L., Davis, J.A., and Luoma, S.N., 1989, Trace metal associations in the water column of south San Francisco Bay, California: Estuarine, Coastal and Shelf Science, v. 28, p. 307-325.

Kuwabara, J.S., Chang, C.C.Y., Khechfe, A.I., and Hunter, Y.R., 1996, Importance of dissolved sulfides and organic substances in controlling the chemical speciation of heavy metals in San Francisco Bay, in Hollibaugh, J.T., ed., San Francisco Bay – the Ecosystem: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 157-172.

Kuwabara, J.S., and Harvey, R.W., 1990, Application of a hollow-fiber, tangential-flow device for sampling suspended bacteria and particles from natural waters: Journal of Environmental Quality v. 19, no. 3, p. 625-629.

Kuwabara, J.S., and Luther, G.W. III, 1993, Dissolved sulfides in the toxic water column of San Francisco Bay, California: Estuaries, v. 16, no. 3A, p. 567-583.

Kuwabara, J.S., Nichols, F.H., Kuivila, K.M., and DiLeo, J.S., 1999, Understanding the human influence on the San Francisco Bay-Delta estuary ecosystem – The Toxic Substances Hydrology (Toxics) Program and Integrated Natural Resource Science (INATURES) Program provide complimentary approaches and results, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2—Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 109-113.

Kuwabara, J.S., Topping, B.R., Coale, K.H., and Berelson, W.M., 1999, Processes affecting the benthic flux of trace metals into the water column of San Francisco Bay, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2—Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 115-119.

Kuwabara, J.S., van Geen, A., McCorkle, D.C., Bernhard, J.M., Zheng, Y., and Topping, B.R., 1999, Redox gradients in the vicinity of the Santa Barbara basin: application of techniques developed within the San Francisco Bay toxics study, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2—Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 121-130.

Lacy, J.R., Schoellhamer, D.H., and Burau, J.R., 1996, Suspended-solids flux at a shallow-water site in south San Francisco Bay, California: Proceedings of the North American Water and Environment Congress, Anaheim, Calif., June 24-28, 1996.

Lee, B.-G., Griscom, S.B., Lee, J-S., Choi, H.J., Koh, C-H., Luoma, S.N., and Fisher, N.S., 2000, Influences of dietary uptake and reactive sulfides on metal bioavailability from aquatic sediments: Science, v. 287, p. 282-284.

Lee, B-G, Wallace, W.G., and Luoma, S.N., 1998, Uptake and loss kinetics of Cd, Cr and Zn in the bivalves Potamocorbula amurensis and Macoma balthica: effects of size and salinity: Marine Ecology Progress Series, v. 175, p. 177-189.

Lionberger, M.A., and Schoellhamer, D.H., 2003, A tidally averaged sediment transport model of San Francisco Bay, California: Proceedings of the 6th biennial State-of-the-Estuary Conference, Oakland, California, October 21-23, 2003, p. 118.

Lionberger, M.A., and Schoellhamer, D.H., 2006, A box model of a series of salt ponds in the Alviso Salt Pond Complex, South San Francisco Bay: Proceedings of the South Bay Science Symposium, June 6, 2006, San Jose, California, p. 15.

Lionberger, M.A., Ganju, N.K., Schoellhamer, D.H., Downing, B.D., Bergamaschi, B.A., and Wheeler, G.A., 2004, Wetland fluxes of dissolved organic carbon and sediment at Browns Island, California: Proceedings of the 2004 CALFED Science Conference, Sacramento, California, October 4-6, 2004, p. 329.

Lionberger, M.A., Schoellhamer, D.H., Oram, J., and May, C., 2006, A tidally averaged sediment-transport model of San Francisco Bay, California: Proceedings of the 8th Federal Interagency Sediment Conference, April 2-6, 2006, Reno, Nevada.

Lionberger, M.A., Schoellhamer, D.H., Buchanan, P.A., and Meyer, S., 2004, Salt-Pond Box Model (SPOOM) and its Application to the Napa-Sonoma Salt Ponds, San Francisco Bay, California: U.S. Geological Survey Water-Resources Investigations Report 03-4199.

Lopez, C. B., Cloern, J.E., Schraga, T.S., Little, A.J., Lucas, L.V., Thompson, J.K., and Burau, J.R., 2006,  Ecological values of shallow-water habitats: implications for restoration of disturbed ecosystems, Ecosystems 9: 422-440.

Lucas, L.V., and Cloern, J.E., 2002, Effects of tidal shallowing and deepening on phytoplankton dynamics: a modeling study: Estuaries, v. 25, p. 497-507.

Lucas, L.V., Cloern, J.E., Koseff, J.R., Monismith, S.G., and Thompson, J.K., 1998, Does the Sverdrup critical depth model explain bloom dynamics in estuaries?: Journal of Marine Research, v. 56, no. 2, p. 375-415.

Lucas, L.V., Cloern, J.E., Thompson, J.K., and Monsen, N.E., 2002, Functional variability of shallow tidal habitats in the Sacramento-San Joaquin Delta: restoration implications: Ecological Applications v. 12, no. 5, p. 1,528-1,547.

Lucas, L.V., Koseff, J.R., Cloern, J.E., Monismith, S.G., and Thompson, J.K., 1999, Processes governing phytoplankton blooms in estuaries, I, the local production-loss balance: Marine Ecology Progress Series, v. 187, p. 1-15.

Lucas, L.V., Koseff, J.R., Monismith, S.G., Cloern, J.E., and Thompson, J.K., 1999, Processes governing phytoplankton blooms in estuaries, II, the role of horizontal transport: Marine Ecology Progress Series, v. 187, p. 17-30.

Lucas, L. V., Sereno, D.M., Burau, J.R., Schraga, T.S., Lopez, C.B., Stacey, M.T., Parchevsky, K.V., and Parchevsky, V.P.,  2006, Intra-daily variability of water quality in a shallow tidal lagoon: mechanisms and implications, Estuaries and Coasts 29(5): 711-730.

Ludwig, Frank L., Cheng, Ralph T., Feinstein, J., Sinton, D., and Becker, A., 1997, An on-line diagnostic wind model applied to San Francisco Bay region—13th International Conference on Interactive Information and Processing System (IIPS) for Meteorology, Oceanography and Hydrology: American Meteorological Society, February 2-7, 1997.

Lundquist, J.D., and Cayan, D.R., 2007, Surface temperature patterns in complex terrain: Daily variations and long-term change in the central Sierra Nevada, California. J. Geophys. Res., 112, D11124, doi:10.1029/2006JD007561.

Lundquist, J.D., Cayan, D.R., and Dettinger, M.D., 2003, Meteorology and hydrology in Yosemite National Park: A sensor network application, in F. Zhao and L.Guibas (eds.), Information Processing in Sensor Networks:  Springer-Verlag, 518-528.

Lundquist, J.D., Cayan, D.R., and Dettinger, M.D., 2004, Spring onset in the Sierra Nevada—When is snowmelt independent of elevation?: J. Hydrometeorology, 5, 325-340.

Lundquist, J.D., and Dettinger, M.D., 2003, Linking diurnal cycles in river flow to interannual variations in climate: American Meteorological Society, 83rd Annual Meeting, 17th Conference on Hydrology, Long Beach, Calif., February 8-13, 2003, p. J2.4-1 to J2.4-5.

Lundquist, J.D., and Dettinger, M.D., 2005, How snowpack heterogeneity affects diurnal streamflow timing: Water Resources Research, 41, W05007, doi:10.1029/2004WR003649, 14 p.

Lundquist, J.D., Dettinger, M.D., and Cayan, D.R., 2005, Snow-fed streamflow timing at different basin scales: Case study of the Tuolumne River above Hetch Hetchy, Yosemite, California: Water Resources Research, 41, W07005, doi:10.1029/2004WR003933, 14 p.

Luoma, S.N., 1986, A comparison of two methods for determining copper partitioning in oxidized sediments: Marine Chemistry, v. 20, p. 45-55.

Luoma, S.N., 1989, Processes affecting metal concentrations in estuarine and coastal marine sediments, in Furness, R.W., and Rainbow, P.S., ed., Heavy Metals in Marine Environment: CRC Press, Boca Raton, Fla., p. 51-66.

Luoma, S.N., 1990, Processes affecting metal concentrations in estuarine and coastal marine sediments, in Furness, R.W., and Rainbow, P.S., eds., Heavy Metals in the Marine Environment: CRC Press, Boca Raton, Fla., p 52-66.

Luoma, S.N., 1995, Pathway models could aid management of contaminants: Interagency Ecological Program for the Sacramento–San Joaquin Estuary Newsletter: California Department of Water Resources, p. 6-8.

Luoma, S.N., 1995, Prediction of metal toxicity in nature for bioassays: limitations and research needs, in Tessier, A., and Turner, D., eds., Metal Speciation and Bioavailability in Aquatic Systems: International Union Pure and Applied Chemistry Series on Chemistry of Environmental Systems, J. Wiley & Sons, New York, p. 609-659.

Luoma, S.N., 1996, The developing framework of ecotoxicology: pollutants as a variable in marine ecosystems?: Journal of Experimental Marine Biology and Ecology, v. 200, p. 29-55.

Luoma, S.N., 1999, Emerging contaminant issues from an ecological perspective, in Morganwalp, D.W., and Buxton, H.T., eds., Proceedings of the U.S. Geological Survey Toxic Substances Hydrology Program, v. 2—Contamination of Hydrologic Systems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 3-6.

Luoma, S.N., and Bryan, G.W., 1979, Trace metal bio-availability – modeling chemical and biological interactions of sediment bound zinc: American Chemical Society Symposium Series 93, p. 577-609.

Luoma, S.N., Bryan, G.W., and Ho, Y.B., 1995, Fate bioavailability and toxicity of silver in estuarine environments: Marine Pollution Bulletin, v. 31, p. 44-54.

Luoma, S.N., and Cain, D.J., 1979, Fluctuations of copper, zinc, and silver in tellenid clams as related to fresh-water discharge–south San Francisco Bay, in Conomos, T.J., ed., San Francisco Bay – The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 231-246.

Luoma, S.N., Cain, D.J., and Johnansson, C., 1985, Temporal fluctuations of silver, copper and zinc in the bivalve Macoma balthica at five stations in south San Francisco Bay: Hydrobiologia, v. 129, p. 109-120.

Luoma, S.N., Cain, D.J., Brown, C., and Axtmann, E.V., 1991, Trace metals in clams (Macoma balthica) and sediments at the Palo Alto mudflat in south San Francisco Bay: April 1990-April 1991: U.S. Geological Survey Open-File Report 91-460, 47 p.

Luoma, S.N., Cain, D.J., Brown, C., and Hornberger, M., 1993, Trace metals in clams (Macoma balthica) and sediments at the Palo Alto mudflat in south San Francisco Bay: June 1992-May 1993: U.S. Geological Survey Open-File Report 93-500, 52 p.

Luoma, S.N., Cain, D.J., Brown, C., Hornberger, M., 1991, Near field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto and San Jose/Sunnyvale water quality control plants in south San Francisco Bay: U.S. Geological Survey Open-File Report 91-460, 47 p.

Luoma, S.N., Cain, D.J., Brown, C., Hornberger, M., 1992, Near field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto and San Jose/Sunnyvale water quality control plants in south San Francisco Bay: U.S. Geological Survey Open-File Report 92-456, 51 p.

Luoma, S.N., Cain, D.J., Brown, C., Hornberger, M., 1993, Near field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto and San Jose/Sunnyvale water quality control plants in south San Francisco Bay: U.S. Geological Survey Open-File Report 93-500, 49 p.

Luoma, S.N., Cain, D.J., Brown, C., Hornberger, M., 1995, Near field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto and San Jose/Sunnyvale water quality control plants in south San Francisco Bay: U.S. Geological Survey Open-File Report 95-299, 83 p.

Luoma, S.N., Cain, D.J., Brown, C., Hornberger, M., 1996, Near field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto and San Jose/Sunnyvale water quality control plants in south San Francisco Bay: U.S. Geological Survey Open-File Report 96-203, 90 p.

Luoma, S.N., Cain, D.J., Brown, C., Hornberger, M., 1997, Near field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto and San Jose/Sunnyvale water quality control plants in south San Francisco Bay: U.S. Geological Survey Open-File Report 97-585, 90 p.

Luoma, S.N., Cain, D.J., Ho, K., and Hutchinson, A., 1983, Variable tolerance to copper in two species from San Francisco Bay: Marine Environmental Research, v. 10, p. 209-222.

Luoma, S.N., and Carter, J.L., 1991, Effects of trace metals on aquatic benthos, in Newmand, M., and McIntosh, A., eds., Metal Ecotoxicology: Concepts & Applications: CRC Press, Boca Raton, Fla., p. 261-300.

Luoma, S.N., Cascos, P.V., and Dagovitz, R.M., 1984, Trace metals in Suisun Bay, California: a preliminary report: U.S. Geological Survey Water Resources Investigations Report 84-4170, 35 p.

Luoma, S.N., and Cloern, J.E., 1982, The impact of waste-water discharge on biological communities in San Francisco Bay, in Kockelman, W.J., ed., San Francisco Bay – Use and Protection: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 137-160.

Luoma, S.N., Dagovitz, R., and Axtmann, E., 1990, Temporally intensive study of trace metals in sediments and bivalves from a large river-estuarine system: Suisun Bay/Delta in San Francisco Bay: The Science of the Total Environment, v. 97/98, p. 685-712.

Luoma, S.N., and Fisher, N.S., 1996, Uncertainties in assessing contaminant exposure from sediments, in Biddinger, G.R., Dillon, T., and Ingersoll, C.G., eds., Ecological Risk Assessments of Contaminated Sediments: SETAC Special Publication Series, Pensacola, Fla., Chapter 14.

Luoma, S.N., and Fisher, N.S., 1997, Uncertainties in assessing contaminant exposure from sediments, in Ingersoll, C.G., Dillon, T., and Biddinger, G.R., eds., Ecological Risk Assessments of Contaminated Sediments: SETAC Special Publication Series, SETAC Press, Pensacola, Fla., p. 211-238.

Luoma, S.N., and Ho, K.T., 1993, Appropriate uses of marine and estuarine sediment bioassays, in Calow, P., ed., Handbook of Ecotoxicology: Blackwell Scientific Publications, p. 193.

Luoma, S.N., Johns, C., Fisher, N.S., Steinberg, N.A., Oremland, R.S., and Reinfelder, J.R., 1992, Determination of selenium bioavailability to a benthic bivalve from particulate and solute pathways: Environmental Science and Technology, v. 26, p. 485-491.

Luoma, S.N., and Linville, R., 1996, A comparison of selenium and mercury concentrations in transplanted and resident bivalves from north San Francisco Bay, in Regional Monitoring Program for Trace Substances: 1995 Annual Report, San Francisco Estuary Institute, Richmond, Calif., p. 160-170.

Luoma, S.N., and Linville, R., 1997, A comparison of selenium and mercury concentrations in transplanted and resident bivalves from north San Francisco Bay, in Regional Monitoring for Trace Substances: 1996 Annual Report, San Francisco Estuary Institute, Richmond, Calif., p. 160-170.

Luoma, S.N., and Linville, R., 1997, Selenium trends in north San Francisco Bay: Interagency Ecological Program for the Sacramento–San Joaquin Estuary Newsletter, v. 10, p. 25-26.

Luoma, S.N., and Nichols, F.H., 1996, Challenges in detecting contaminant effects on an estuarine ecosystem affected by many disturbances, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Colorado Springs, Colo., September 20-24, 1993: U.S. Geological Survey Water Resources Investigations Report 94-4015, p. 689-694.

Luoma, S.N., and Phillips, D.J.H., 1988, Distribution, variability, and impacts of trace elements in San Francisco Bay: Marine Pollution Bulletin, v. 19, p. 413-425.

Luoma, S.N., van Geen, A., Lee, B.-G., and Cloern, J.E., 1998, Metal uptake by phytoplankton during a bloom in south San Francisco Bay: Implications for metal cycling in estuaries: Limnology and Oceanography, v. 43, no. 5, p. 1,007-1,016.

Luoma, S.N., with 20 other contributors, 1997, Reassessment of metals criteria for aquatic life protection: Proceedings, SETAC Pellston Conference, 1996, Bergman, H.L., and Dorward-King, E.J., eds., SETAC Press, Pensacola, Fla., 114 p.

MacCoy, D., Crepeau, K.L., and Kuivila, K.M., 1995, Dissolved pesticide data for the San Joaquin River at Vernalsi and the Sacramento River at Sacramento, California, 1991-1994: U.S. Geological Survey Open-File Report 95-110, 27 p.

Malamud-Roam, F., Dettinger, M.D., Ingram, B.L., Hughes, M., and Florsheim, J., 2007, Holocene climates and connections between the San Francisco Bay estuary and its watershed—A review: San Francisco Estuary and Watershed Science, 5(1), 28 p.

Maresca, J.W., Padder, R.R., Cheng, R.T., and Siebel, E., 1980, High frequency radar measurements of tidal currents flowing through San Pablo Strait, San Francisco Bay: Limnology and Oceanography, v. 25, no. 5, p. 929-935.

Marvin-DiPasquale, M., Agee, J., Bouse, R., Jaffe, B., 2003, Microbial cycling of mercury in contaminated wetland and open-water sediments of San Pablo Bay, California: Environmental Geology, v. 43, no. 3, p. 260-267.

Maurer, E.P., Stewart, I.T., Bonfils, C., Duffy, P.B., and Cayan, D.R.,2007, Detection, attribution, and sensitivity of trends toward earlier streamflow in the Sierra Nevada. J. Geophys. Res., 112, D11118, doi:10.1029/2006JD008088.

May, C.L., Koseff, J.R., Lucas, L.V., Cloern, J.E., and Schoellhamer, D.H., 2003, Effects of spatial and temporal variability of turbidity on phytoplankton blooms, Marine Ecology Progress Series 254: 111-128.

McBride, G.B., Vant, W.N., Cloern, J.E., and Liley, J.B., 1993, Development of a model of phytoplankton blooms in Manukau Harbour: National Institute of Water and Atmospheric Research, Ecosystems Publication no. 3, Hamilton, New Zealand, 52 p.

McCabe, G.J., and Dettinger, M.D., 1999, Decadal variations in the strength of ENSO teleconnections with precipitation in the Western United States: International Journal of Climatology, v. 19, p. 1,399-1,410.

McCabe, G.J., and Dettinger, M.D., 2002, Primary modes and predictability of year-to-year snowpack variations in the western United States from teleconnections with Pacific Ocean climate: Journal of Hydrometeorology, v. 3, p. 13-25.

McCulloch, D.S., Peterson, D.H., Carlson, P.R., and Conomos, T.J., 1970, Some effects of fresh-water inflow on the flushing of south San Francisco Bay – a preliminary report: U.S. Geological Survey Circular 637A, 27 p.

McDonald, E.T., and Cheng, R.T., 1994, Issues related to modeling the transport of suspended sediments in northern San Francisco Bay, California, in The Proceedings of the Third International Conference on Estuarine and Coastal Modeling: American Society of Civil Engineers, Chicago, Ill., p. 551-564.

McDonald, E.T., and Cheng, R.T., 1997, A numerical model of sediment transport applied to San Francisco Bay, California: Journal of Marine Environmental Engineering, v. 4, p. 1-41.

McGann, Mary, 1995, 3500-year B.P. record of climatic change in estuarine deposits of south San Francisco Bay, California, in Sanginés, E.M., Andersen, D.W., and Buising, A.V., eds., Recent geologic studies in the San Francisco Bay area: Pacific Section, Society of Sedimentary Geology (SEPM), v. 76, p. 225-236.

McGann, Mary, and Sloan, Doris, 1996, Recent introduction of the foraminifer Trochammina hadai Uchio into San Francisco Bay, California, USA: Marine Micropaleontology, v. 28, no. 1, p. 1-3.

McGann, Mary, and Sloan, Doris, 1999, Benthic foraminifers in the regional monitoring program's San Francisco Estuary samples, in 1997 Annual Report for the Regional Monitoring Program for Trace Substances in the San Francisco Estuary: San Francisco Estuary Institute, Richmond, Calif., p. 249-258.

McGann, Mary, Sloan, Doris, and Cohen, Andrew N., 2000, Invasion by a Japanese marine microorganism in western North America: Hydrobiologia, v. 421, p. 1-6.

McGann, Mary, Sloan, Doris, and Wan, Elmira, in press, Biostratigraphy beneath central San Francisco Bay along the San Francisco-Oakland Bay Bridge project: U.S. Geological Survey Professional Paper.

McKee, L.J., Ganju, N.K., Schoellhamer, D.H., 2006, Estimates of suspended sediment flux entering San Francisco Bay from the Sacramento and San Joaquin Delta, San Francisco Bay, California: Journal of Hydrology, v. 323, p. 335-352.

McKee, L., Ganju, N., Schoellhamer, D., Davis, J., Yee, D., Leatherbarrow, J., and Hoenicke, R., 2002, Estimates of suspended sediment flux entering San Francisco Bay from the Sacramento and San Joaquin Delta: Report prepared for the Sources Pathways and Loading Workgroup of Regional Monitoring Program for Trace Substances in the San Francisco Estuary, San Francisco Estuary Institute, Oakland, California, 28 p.

Meyers, W.J., and Kuivila, K.M., 1996, Method for estimating the activity of carbofuran-degrading microorganisms in environmental samples, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program, Proceedings of the Technical Meeting, Colorado Springs, Colo., September 20-24, 1993: U.S. Geological Survey Water Resources Investigations Report 94-4015, p. 719-723.

Miles, A.K., Lawler, S.P., Dritz, D., and Spring, S., 2002, Effects of mosquito larvicide on mallard ducklings and prey: Wildlife Society Bulletin, v. 30, no. 3, p. 675-682.

Miles, A.K., Ricca, M.A., Spring, S.E., Morris, C., Wilcox, C., and Maurer, T. 2007, Mercury in sediments, Alviso and Eden Landing salt ponds, south San Francisco Bay, California, Society of Wetland Scientists International Conference, Sacramento, CA., June 2007, p 60.

Miles, A.K., Spring, S.E., Ricca, M.A., Takekawa, J.T., Athearn, N.D., and Schoellhamer, D.H., 2007, Spatial and temporal structure of macroinvertebrate assemblages, San Francisco Bay salt ponds, Society of Wetland Scientists International Conference, Sacramento, CA., June 2007, p 51.

Miles, A.K., Takekawa, J.Y., Schoellhamer, D.H., Athearn, N.D., Saiki, M.K., Duffy, W.D., Kleinschmidt, S., Shellenbarger, G.G., Jannusch, C.A., Spring, S.E., 2005, Ecological structure of salt ponds, San Francisco Bay, California: balancing tidal wetland restoration with existing beneficial habitat, The American Society of Limnology and Oceanography Aquatic Sciences Meeting 2005, Salt Lake City, UT., February 2005, p?.

Miles, A.K., Takekawa, J.Y., Schoellhamer, D.H., Lu, C.T., Duffy, W.G., and Saiki, M.K., 2000, Science support for wetland restoration in the Napa-Sonoma salt ponds, San Francisco Bay estuary, 1999 progress report: Unpublished Progress Report: U.S. Geological Survey, Davis and Vallejo, Calif., 57 p.

Miles, A.K., Takekawa, J.Y., Schoellhamer, D.H., Spring, S.E., Athearn, N.D., Shellenbarger, G.G., and Tsao, D.C., 2004, San Francisco Bay Estuary Salt Ponds Progress Report 2001 – 2003, Priority Ecosystem Science Program, USGS/USFWS (CNO) Science Support Program. Unpublished Progress Report, U.S. Geological Survey, Davis and Vallejo, CA. 67p.

Miller, L.G., Coutlakis, M.D., Oremland, R.S., and Ward, B.B., 1993, Selective inhibition of ammonium oxidation and nitrification-linked N²0 formation by methyl fluoride and dimethyl ether: Applied and Environmental Microbiology, v. 59, p. 2,457-2,464.

Miller, L.G., Oremland, R.S., and Paulsen, S., 1986, Measurement of N20 reductase activity in aquatic sediments: Applied and Environmental Microbiology, v. 51, p. 18-24.

Monismith, S., Burau, J., and Stacey, M., 1996, Stratification dynamics and gravitational circulation in northern San Francisco Bay: Environmental Fluid Mechanics Laboratory, Stanford University, p. 123-155.

Monismith, S.G., Kimmerer, W., Burau, J.R., and Stacey, M.T., 2002, Structure and flow-induced variability of the subtidal salinity field in northern San Francisco Bay: American Meteorological Society, p. 3,003-3,019.

Monismith, S.G., Koseff, J.R., Thompson, J.K., O'Riordan, C.A., Nepf, H.M., 1990, A study of model bivalve siphonal currents: Limnology and Oceanography, v. 35, no. 3, p. 376-392.

Monsen, N.E., Cloern, J.E., Lucas, L.V., and Monismith, S.G., 2002, A comment on the use of flushing rate, residence time, and age as transport time scales: Limnology and Oceanography, v. 47, p. 1,545-1,553.

Monsen, N.E., Cloern, J.E., and Burau. J.R., 2007, Effects of Flow Diversions on Water and Habitat Quality; Examples from California's Highly Manipulated Sacramento-San Joaquin Delta: San Francisco Estuary and Watershed Science. Vol. 5, Issue 3 (July 2007), Article 2.

Moon, G.E., Kuivila, K., Ruhl, C., and Schoellhamer, D., 2000, Exposure of Delta Smelt to dissolved pesticides in 1998 and 1999: Interagency Ecological Program Newsletter, v. 13, no. 4, p. 27-33.

Moon, G.E., Shouse, M.K., Parchaso, F. Thompson, J. K., Luoma, S.N., Cain, D.J. and Hornberger, M.I., 2005, Near-field receiving water monitoring of trace metals and a benthic community near the Palo Alto Water Quality Control Plant in South San Francisco Bay: 2004, U.S. Geological Survey Open File Report 2005-1279. Menlo Park, California. 118p.

Nichols, F.H., 1973, A review of benthic faunal surveys in San Francisco Bay: U.S. Geological Survey Circular 677, 20 p.

Nichols, F.H., 1977, Infaunal biomass and production on a mud flat, San Francisco Bay, California, in Coull, B.C., ed., Ecology of Marine Benthos: University of South Carolina, Columbia, p. 339-357.

Nichols, F.H., 1979, Natural and anthropogenic influences on benthic community structure in San Francisco Bay, in Conomos, T.J., ed., San Francisco Bay – The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 409-426.

Nichols, F.H., 1984, Significance of long-term variations in estuarine benthos: U.S. Geological Survey Circular 938, p. 91-97.

Nichols, F.H., 1985, Abundance fluctuations among benthic invertebrates in two Pacific estuaries: Estuaries, v. 8, p. 136-144.

Nichols, F.H., 1985, Increased benthic grazing: An alternative explanation for low phytoplankton biomass in northern San Francisco Bay during the 1976-77 drought: Estuarine, Coastal and Shelf Science, v. 21, p. 379-388.

Nichols, F.H., 1987, Benthic ecology and heavy metal accumulation, in Goodrich, D.M., ed., San Francisco Bay – Issues, resources, status, and management: National Oceanic and Atmospheric Administration Estuary of the Month Seminar Series, no. 6, p. 65-68.

Nichols, F.H., 1989, The San Francisco Bay estuary – an overview: Proceedings of the Fourth Biennial Oceanic Society State of the Bay Conference, San Francisco, Calif., April 1989, p. 11-18.

Nichols, F.H., 1994, San Francisco Bay estuary and delta ecosystem: U.S. Geological Survey Open-File Report 94-98, 2 p.

Nichols, F.H., 1995, The San Francisco bay and delta: an estuary undergoing change: U.S. Geological Survey 1994 Yearbook, p. 39-42.

Nichols, F.H., 1995, USGS supports ecosystem management in the San Francisco bay and delta: Interagency Ecological Program for the Sacramento–San Joaquin Estuary Newsletter, Summer 1995, Sacramento, Calif., p. 10-11.

Nichols, F.H., 1998, Integrated natural resource science program – San Francisco Bay program: U.S. Geological Survey Fact Sheet FS-138-98.

Nichols, F.H., Cloern, J.E., Luoma, S.N., and Peterson, D.H., 1986, The modification of an estuary: Science, v. 231, p. 567-573.

Nichols, F.H., and Luoma, S.N., 1997, Long-term investigations provide fundamental insight into natural and human-induced change in the San Francisco Bay (U.S.A.) estuary, in Keegan, B.F., Lambshead, P.J.D., Coull, B.C., Overcash, M., and Nolan, C., eds., Change in marine benthos: the case for long-term studies—Proceedings of a Workshop on Long Term Study Influences on Science and Policy, Galway, Ireland, 1994: European Commission Environment Research Programme, Ecosystems Research Report 16, p. 37-53.

Nichols, F.H., and Pamatmat, M.M., 1988, The ecology of the soft-bottom benthos of San Francisco Bay: A community profile: U.S. Fish Wildlife Service Biology Report, v. 85, no. 7.19, 73 p.

Nichols, F.H., and Thompson, J.K., 1982, Seasonal growth in the bivalve Macoma balthica near the southern limit of its range: Estuaries, v. 5, p. 110-120.

Nichols, F.H., and Thompson, J.K., 1985, Persistence of an introduced mud flat community in south San Francisco Bay, California: Marine Ecology Progress Series, v. 24, p. 83-97.

Nichols, F.H., and Thompson, J.K., 1985, Time scales of change in the San Francisco Bay benthos: Hydrobiologia, v. 129, p. 121-138.

Nichols, F.H., Thompson, J.K., and Schemel, L.E., 1990, Remarkable invasion of San Francisco Bay (California, USA) by the asian clam Potamocorbula amurensis, II, Displacement of a former community: Marine Ecology Progress Series, v. 66, p. 95-101.

Ning, X., Cloern, J.E., and Cole, B.E., 2000, Spatial and temporal variability of picocyanobacteria Synechococcus sp. in San Francisco Bay: Limnology and Oceanography, v. 45, no. 3, p. 695-702.

Oltmann, R.N., 1993, Continuous flow measurements using fixed ultrasonic meters: Interagency Ecological Program for the Sacramento–San Joaquin Estuary Newsletter, summer 1993, p. 4.

Oltmann, R., 1995, Continuous flow measurements using ultrasonic velocity meters – an update: Interagency Ecological Program Newsletter, Autumn 1995, p. 22-25.

Oltmann, R.N., 1995, Hydrodynamics of California's Sacramento-San Joaquin Delta, and the collection of flow data for the tracking of pesticides, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program–Proceedings of the Technical Meeting, Colorado Springs, Colo., September 20-24, 1993.

Oltmann, R.N., 1996, Hydrodynamics of California's Sacramento-San Joaquin Delta, and the collection of flow data for the tracking of pesticides, in Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program–Proceedings of the Technical Meeting, Colorado Springs, Colo., September 20-24, 1993: U.S. Geological Survey Water Resources Investigations Report 94-4015, p. 695-698.

Oltmann, R.N., 1996, Sediment inflow to the delta from the Sacramento and San Joaquin Rivers: Interagency Ecological Program for the Sacramento–San Joaquin Estuary Newsletter, v. 8-2, spring 1996, p. 22-23.

Oltmann, R.N., 1996-99, Interagency Program Quarterly Highlights – Delta Flow Measurements: Interagency Ecological Program Newsletter, quarterly reports.

Oltmann, R.N., 1998, Indirect measurement of Delta outflow using ultrasonic velocity meters and comparison with mass-balance calculated outflow: Interagency Ecological Program Newsletter, v. 11-1, winter 1998, p. 5-8.

Oltmann, R.N., 1998, Measured flow and tracer-dye data showing anthropogenic effects on the hydrodynamics of south Sacramento-San Joaquin Delta, California, spring 1996 and 1997: U.S. Geological Survey Open-File Report 98-285, 16 p.

Oltmann, R.N., 1999, Measured flow and tracer-dye data for spring 1996 and 1997 for the south Sacramento-San Joaquin Delta, California: Interagency Ecological Program Newsletter, v. 12, no. 3, summer 1999 p. 37-44.

Oltmann, R.N., 1999, Sediment inflow to the Sacramento-San Joaquin Delta and the San Francisco Bay: Interagency Ecological Program Newsletter, v. 12-1,winter 1999, p. 30-33.

Oltmann, R.N., Schoellhamer, D.H., and Dinehart, R.L., 1999, Sediment inflow to the Sacramento-San Joaquin Delta and the San Francisco Bay: Interagency Ecological Program Newsletter, v. 12, no. 1, p. 30-33.

Oremland, R.S., 1979, Methanogenic activity in plankton samples and fish intestines: a mechanism for in-situ methanogenesis in oceanic surface waters: Limnology and Oceanography, v. 24, p. 1,136-1,141.

Oremland, R.S., 1981, Microbial formation of ethane in anoxic estuarine sediments: Applied and Environmental Microbiology, v. 42, p. 122-129.

Oremland, R.S., and Culbertson, C.W., 1992, Evaluation of methyl fluoride and dimethyl ether as inhibitors of aerobic methane oxidation: Applied and Environmental Microbiology, v. 58, p. 2,983-2,992.

Oremland, R.S., and Culbertson, C.W., 1992, Importance of methane-oxidizing bacteria in the methane budget as revealed by the use of a specific inhibitor: Nature, v. 356, p. 421-423.

Oremland, R.S., and Polcin, S., 1982, Methanogenesis and sulfate reduction – Competitive and non-competitive substrates in estuarine sediments: Applied and Environmental Microbiology, v. 44, p. 1,270-1,276.

Oremland, R.S., and Zehr, J.P., 1986, Formation of methane and carbon dioxide from dimethylselenide in anoxic sediments and by a methanogenic bacterium: Applied and Environmental Microbiology, v. 52, no. 5, p. 1,031-1,036.

Oremland, R.S., Cloern, J.E., Sofer, Z., Smith, R.L., Culbertson, C.W., Zehr, J., Miller, L., Cole, B., Harvey, R., Iversen, N., Klug, M., Des Marais, D.J., and Rau, G., 1988, Microbial and biogeochemical processes in Big Soda Lake, Nevada: Geological Society Special Publication, no. 40, p. 59-75.

Oremland, R.S., Culbertson, C.W., and Winfrey, M.R., 1991, Methylmercury decomposition in sediments and bacterial cultures: involvement of methanogens and sulfate reducers in oxidative demethylation: Applied and Environmental Microbiology, v. 57, p. 130-137.

Oremland, R.S., Hollibaugh, J.T., Maest, A.S., Presser, T., Miller, L.G., and Culbertson, C.W., 1989, Selenate reduction to elemental selenium by anaerobic bacteria in sediments and culture: biogeochemical significance of a novel, sulfate-independent respiration: Applied and Environmental Microbiology, v. 69, no. 44, p. 2,333-2,343.

Oremland, R.S., Kiene, R.P., Mathrani, I., Whiticar, M., and Boone, D.R., 1989, Description of an estuarine methylotrophic methanogen, which grows on dimethyl sulfite: Applied and Environmental Microbiology, v. 55, no. 4, p. 994-1,002.

Oremland, R.S., Marsh, L., and Polcin, S., 1982, Methane production and simultaneous sulfate reduction in anoxic, salt marsh sediments: Nature, v. 296, p. 143-145.

Oremland, R.S., Umberger, C., and Culbertson, C., 1984, Dentrification in San Francisco Bay intertidal sediments: Applied and Environmental Microbiology, v. 47, p. 1,106-1,112.

Oremland, R.S., Whiticar, M.J., Strohmaier, F.E., and Kiene, R.P., 1988, Bacterial ethane formation from reduced, ethylated sulfur compounds in anoxic sediments: Geochimica et Cosmochimica Acta, v. 52, p. 1,895-1,904.

Orlando, J.L., and Kuivila, K.M., 2004, Changes in rice pesticide use and surface water concentrations in the Sacramento River watershed, California: U.S. Geological Survey Scientific Investigations Report 2004–5097, 28 p.

Orr, M., May, C., Williams, P., Lionberger, M., Schoellhamer, D., Rottenborn, S., Duke, R., Stralberg, D., Herzog, M., and Ritchie, S., 2005, Tools for assessing landscape-scale habitat changes in wetland restoration planning: Proceedings of the 7th biennial State-of-the-Estuary Conference, Oakland, California, October 4-6, 2005, p. 31.

Ota, A.Y., Schemel, L.E., and Hager, S.W., 1986, Physical and chemical data for northern San Francisco Bay, California, September-November, 1984: U.S. Geological Survey Open-File Report 86-228, 32 p.

Ota, A.Y., Schemel, L.E., and Hager, S.W., 1986, Physical and chemical data for the Sacramento River at Rio Vista, California, November, 1983 – November, 1984: U.S. Geological Survey Open-File Report 86-229, 33 p.

Ota, A.Y., Schemel, L.E., and Hager, S.W., 1989, Physical and chemical properties of San Francisco Bay, California, 1980: U.S. Geological Survey Open-File Report 89-421, 251 p.

Pagano, T., Pasteris, P., Dettinger, M., Cayan, D., and Redmond, K., 2004, Spring 2004 — Western water managers feel the heat: Eos, v. 85, pp. 385, 392-393.

Parchaso, Francis, 1993, Seasonal reproduction of Potamocorbula amurensis in San Francisco Bay, California: California State University, Masters Thesis, 43 p.

Parchaso, F., and Thompson, J.K., 2002, The Influence of hydrologic processes on reproduction of the introduced bivalve Potamocorbula amurensis in northern San Francisco Bay, California: Pacific Science, v. 56, no. 3, p. 329-345.

Parchaso, F., Brown, C.L., Thompson, J.K., Luoma, S.N., 1997, In situ effects of trace contaminants on the ecosystem in the San Francisco Bay estuary, 1995: the necessary link to establishing water quality standards, II: U.S. Geological Survey Open-File Report 97-420.

Parsons, T., Sliter, R., Geist, E.L., Jachens, R.C., Jaffe, B.E., Foxgrover, A., Hart, P.E., and McCarthy, J., 2003, Structure and mechanics of the Hayward-Rodgers Creek fault stepover, San Francisco Bay, California: Bulletin Seismological Society of America, v. 93, no. 5, p. 2,187-2,200.

Pereira, W.E., Domagalski, J.L., Hostettler, F.D., Brown, L.R., and Rapp, J.B., 1996, Occurrence and accumulation of pesticides and organic contaminants in river sediment, water and clam tissues from the San Joaquin River and Tributaries, California: Environmental Toxicology and Chemistry, v. 15, no. 2, p. 172-180.

Pereira, W.E., Hostettler, F.D., Cashman, J.R., and Nishioka, R.S., 1994, Occurrence and distribution of organochlorine compounds in sediment and livers of striped bass (Morone saxatilis) from the San Francisco Bay-Delta Estuary: Marine Pollution Bulletin, v. 28, p 434-441.

Pereira, W.E., Hostettler, F.D., Kvenvolden, K.A., Rosenbauer, R.J., and Murphy, F., 1997, Organic contaminants in peninsula berms and agricultural soils at the Sonoma baylands wetland demonstration project site and adjacent seasonal wetlands, Sonoma County, California: U.S. Geological Survey Open-File Report 97-931.

Pereira, W.E., Hostettler, F.D., Kvenvolden, K.A., Rosenbauer, R.J., and Murphy, F., 1998, Geochemical studies of anthropogenic and natural organic compounds at the Sonoma baylands wetland demonstration project site and adjacent marshlands, Sonoma County, California: U.S. Geological Survey Open-File Report 98-806.

Pereira, W.E., Hostettler, F.D., Luoma, S.N., van Geen, A., Fuller, C.C., and Anima, R.J., 1999, Sedimentary record of anthropogenic and biogenic polycyclic aromatic hydrocarbons in San Francisco Bay, California: Marine Chemistry, v. 64, p. 99-113.

Pereira, W.E., Hostettler, F.D., Rapp J.B., 1996, Distributions and fate of chlorinated pesticides, biomarkers and polycyclic aromatic hydrocarbons in sediments along a contamination gradient from a point-source in San Francisco Bay, California: Marine Environmental Research, v. 41, no. 3, p. 299-314.

Pereira, W.E., Hostettler, F.D., and Rapp, J.B., 1992, Bioaccumulation of hydrocarbons derived from terrestrial and anthropogenic sources in the asian clam, Potamocorbula amurensis, in San Francisco Bay estuary: Marine Pollution Bulletin, v. 24, p. 103-109.

Pereira, W.E., Hostettler, F.D., and Wade, T.L., 1999, Butyltin contamination in sediments and lipid tissues of the asian clam, Potamocorbuls amurensis, near Mare Island naval shipyard, San Francisco Bay: in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program, v. 2–Proceedings of the Technical Meeting, Charleston, S. Carolina, March 8-12, 1999: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 41-49.

Pereira, W.E., Wade, T.L., Hostettler, F.D., and Parchaso, R., 1999, Accumulation of butyltins in sediments and lipid tissues of the asian clam, Potamocorbula amunensis, Near the Mare Island Naval Shipyard, San Francisco Bay, California: Marine Pollution Bulletin, v. 38, p. 1,005-1,010.

Peterson, D.H., 1979, Sources and sinks of biologically reactive oxygen, carbon, nitrogen, and silica in northern San Francisco Bay, in Conomos, T.J., ed., San Francisco Bay - The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, Calif., p. 175-194.

Peterson, D.H., Cayan, D.R., Dettinger, M.D., Noble, M., Riddle, L.G., Schemel, L.E., Smith, R.E., Uncles, R.J., and Walters, R., 1996, San Francisco Bay salinity: Observations, numerical simulation, and statistical models, in Hollibaugh, J.T., ed., San Francisco Bay – The Ecosystem, American Association for the Advancement of Science, Pacific Division, San Francisco p. 9-34.

Peterson, D.H., Cayan, D.R., Dettinger, M., DiLeo, J., Hager, S., Knowles, N., Nichols, F., Schemel, L.E., Smith, R.E., and Uncles, R.J., 1995, FACT SHEET, Seasonal/yearly salinity variation in San Francisco Bay. FS-213-95, 4 p.

Peterson, D.H., Cayan, D.R., DiLeo-Stevens, J., and Ross, T.G., 1987, Some effects of climate variability on hydrology in western North America: IAHS Publication no. 168, p. 45-62.

Peterson, D.H., Cayan, D., DiLeo, J., Noble, M., and Dettinger, M., 1995, The Role of Climate in Estuarine Variability: American Scientist, v. 83, p. 58-67.

Peterson, D.H., Cayan, D.R., and Festa, J.F., 1986, Interannual variability in biochemistry of partially mixed estuaries: Dissolved silicate cycles in northern San Francisco Bay, edited by Wolfe, D.A., in Estuarine Variability, Academic Press, New York, p. 123-138.

Peterson, D.H., Cayan, D.R., Festa, J.F., Nichols, F.H., Walters, R.A., Slack, J.V., Hager, S.E., and Schemel, L.E., 1989, Climate variability in an estuary: effects of riverflow on San Francisco Bay, in Peterson, D.H., ed., Aspects of Climate Variability in the Pacific and the Western Americas: American Geophysical Union, Washington, D.C., p. 419-442.

Peterson, D.H., Cayan, D.R., Smith, R.E., Dettinger, M.D., and Riddle, L., 2001, Retrospective appraisal of the 2000 maximum flow forecasts: Scripps Institution of Oceanography (CAP) California Applications Program (on-line publication)

Peterson, D.H., Cayan, D.R., Smith, R.E., Dettinger, M.D., and Riddle, L., 2002, An experimental forecast of maximum daily snowmelt discharge for the year 2002: Scripps Institution of Oceanography (CAP) California Applications Program (on-line publication)

Peterson, D.H., and Conomos, T.J., 1975, Implications of seasonal chemical and physical factors on the production of phytoplankton in northern San Francisco Bay, in Proceedings, Workshop on Algae Nutrient Relationships in the San Francisco Bay and Delta, 8-10 November 1973, Clear Lake, California: San Francisco Bay and Estuarine Association, San Francisco, p. 147-165.

Peterson, D.H., Conomos, T.J., Broenkow, W.W., and Doherty, P.C., 1975, Location of the non-tidal current null zone in northern San Francisco Bay: Estuarine and Coastal Marine Science, v. 3, p. 1-11.

Peterson, D.H., Conomos, T.J., Broenkow, W.W., and Scrivani, E.P., 1975, Processes controlling the dissolved silica distribution in San Francisco Bay, in Cronin, L.E., ed., Estuarine Research – Chemistry and Biology: Academic Press, p. 153-187.

Peterson, D.H., Dettinger, M.D., Cayan, D.R., DiLeo, J. Isaacs, C., Riddle, L., and Smith, R., 1996, River salinity variations in response to discharge: Examples from Western United States during early 1900s, in Proceedings of the twelfth Annual Pacific Climate (PACLIM) Workshop, Isaacs and Tharp, eds., Technical Report 46 of the Interagency Ecological Program for the Sacramento–San Joaquin Estuary p. 145-153.

Peterson, D.H., Dettinger, M.D., Cayan, D.R., Smith, R.E., Riddle, L., and Knowles, N., 1997, Spring snowmelt in the Sierra Nevada - Does a day make a difference?: Interagency Ecological Program Newsletter, v. 11, no. 3, Summer 1997, p. 16-19.

Peterson, D.H., Dettinger, M.D., Cayan, D.R., Smith, R.E., and Riddle, L., 2000, An organized signal in snowmelt runoff over the Western United States: Journal of the American Water Resources Association, v. 36, no. 2, p. 421-432

Peterson, D.H., and Festa, J.F., 1984, Numerical simulation of phytoplankton productivity in partially mixed estuaries: Estuarine Coastal Shelf Science, v. 19, p. 563-589.

Peterson, D.H., Hager, S.W., Schemel, L.E., and Cayan, D.R., 1987, Riverine, C, N, Si and P transport to the coastal ocean: An overview, in Jansson, Bengt-Owe, Coastal-Offshore Ecosystem Interactions: Lecture Notes on Coastal and Estuarine Studies, v. 22, p. 227-253.

Peterson, D.H., Lundquist, J.D., Stewart, I., Knowles, N., Solomon, M and Hager, S.W., 2005, Sierra Nevada Hydroclimatology:  An experimental prediction of maximum daily snowmelt discharge in 2005, 16 p. (http://meteora.ucsda.edu/cap).

Peterson, D.H., Noble, N., and Smith, R.E., 1993, Suspended Sediment in San Francisco Bay estuary, California—Recent History and Available Data Sets: Water Resources Investigation Report 93-4128, 35 p.

Peterson, D.H., Perry, M.J., Bencala, K.E., and Talbot, M.C., 1987, Phytoplankton productivity in relation to light intensity: A simple equation: Estuarine, Coastal and Shelf Science v. 24, p. 813-832.

Peterson, D.H., Schemel, L.E., Smith, R.E., Harmon, D.D., and Hager, S.W., 1987, The flux of particulate organic carbon in estuaries: U.S. Geological Survey Water Supply Series, Selected Papers in the Hydrologic Sciences, p. 41-49.

Peterson, D.H., Smith, R.E., Dettinger, M., Cayan, D.R., Hager, S.W., and Schemel, L.E., 1999, Forecasting spring discharge in the west: A step towards forecasting stream chemistry. Proceedings of the Technical Meeting Charleston, SC, March 8-12, 1999, U.S. Geological Survey Water Resources Investigations Report 99-4018B, Vol. 2, p. 51-58.

Peterson, D.H., Smith, R.E., Dettinger, M.D., Cayan, D.R., and Riddle, L., 1999, An organized signal in snowmelt runoff over the West: Proceedings, Specialty Conference on Potential Consequences of Climate Variability and Changes to Water Resources of the United States, American Water Resources Association (Brian Adams, ed.), 129-137.

Peterson, D.H., Smith, R.E., Hager, S.W., Harmon, D.D., Herndon, R., and Schemel, L.E., 1985, Interannual variability in dissolved inorganic nutrients in northern San Francisco Bay estuary: Hydrobiologia, v. 129, p. 37-58.

Peterson, D., Smith, R., and Hager, S., 2004, A walk through the hydroclimate network in Yosemite National Park: River Chemistry, Sierra Nature Notes, v. 4.on-line article)

Peterson, D., Smith, R., Hager, S., Cayan, D. and Dettinger, M., 2004, Air temperature and snowmelt discharge characteristics, Merced River at Happy Isles, Yosemite National Park, Central Sierra Nevada, Proceedings of the Twentieth Annual Pacific Climate Workshop, p. 53-64.

Peterson, D.H., Smith, R.E., Hager, S.W., Huber, K., Dettinger, M., and Dileo, J., 2003, Alpine hydroclimatology: exploring the mystery of salinity change in portions of the Stanislaus and Merced Rivers: U.S. Geological Survey General Interest Publication, 24 p.

Peterson, D.H., Smith, R.E., Hager, S.W., Huber, K., Dettinger, M., and DiLeo, J., 2004, Alpine hydroclimatology, exploring the mystery of salinity change in portions of the Stanislaus and Merced Rivers, U.S. Geological Survey Open-File Report, 18 p. and Scripps Institution of Oceanography (CAP) California Applications Programs. http://sfbay.wr.usgs.gov/access/HydroClim/HydroClimTutorial.pdf

Peterson, D.H., Smith, R., Hager, S., Hicke, J.,  Dettinger, M., and Huber, K., 2005, River chemistry as a monitor of Yosemite Park mountain hydroclimates: Eos, Transactions of American Geophysical Union, 86, 285-288.

Peterson, D.H., Smith, R.E., Stewart, I., Knowles, N., Soulard, C., Hager, S., 2005, Snowmelt discharge characteristics Sierra Nevada, California, U.S. Geological Survey Scientific Investigations Report 2005-5056.

Peterson, H.A., 2002, Long-term benthic community change in a highly invaded estuary,  M.A. Thesis, San Francisco State University, 108 p.

Powell, T.M., Cloern, J.E., and Huzzey, L.M., 1989, Spatial and temporal variability in south San Francisco Bay (USA), I, horizontal distributions of salinity, suspended sediments, and phytoplankton biomass and productivity: Estuarine, Coastal and Shelf Science, v. 28, p. 583-597.

Powell, T.M., Cloern, J.E., and Walters, R.A., 1986, Phytoplankton spatial distribution in south San Francisco Bay: mesoscale and small-scale variability, in Wolfe, D.A., ed., Estuarine Variability: Academic Press, New York, p. 369-383.

Powell, T.M., Willmot, S., Murray, J.D., Manoranjan, V.S., and Cloern, J.E., 1988, Transient spatial patterns in plankton communities: blooms and traveling waves of phytoplankton in estuaries, in Hallam, T.G., Gross, L.J., and Levin, S.A., eds., 1986 Proceedings of Triest Research Conference on Mathematical Ecology: World Scientific Publishing, p. 236-267.

Ralph, F.M., Neiman, P.J., Wick, G., Gutman, S., Dettinger, M., Cayan, D., and White, A.B., 2006, Flooding on California’s Russian River—Role of atmospheric rivers: Geophysical Research Letters, 33 (L13801), 5 p, doi:10.1029/2006GL026689.

Ramil, H.R., Buchanan, P.A., Sullivan, B.J., and Brewster, G.D., 2004, Calibration of specific conductance, water-temperature, and turbidity instruments: Proceedings of the 2004 CALFED Science Conference, Sacramento, California, October 4-6, 2004, p. 357.

Reinfelder, J.R., Fisher, N.S., Luoma, S.N., Nichols, J.W., and Wang, W.-X., 1998, Trace element trophic transfer in aquatic organisms: a critique of the kinetic model approach: The Science of the Total Environment, v. 219, no. 2-3, p. 117-135.

Reinfelder, J.R., Wang, W.-X., Luoma, S.N., and Fisher, N.S., 1997, Assimilation efficiencies and turnover rates of trace elements in marine bivalves: a comparison of oysters, clams and mussels: Marine Biology, v. 129, p. 443-452.

Ritson, R.I., Bouse, R.M., Flegal, A.R., and Luoma, S.N., 1999, Stable lead isotopic analyses of historic and contemporary lead contamination of San Francisco Bay estuary: Marine Chemistry, v. 64, nos. 1 & 2, p. 71-83.

Rodgers, K.M., Garrison, D.L., and Cloern, J.E., 1997, Toxic phytoplankton in San Francisco Bay, in 1995 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances: San Francisco Estuary Institute, p. 7.4.1 to 7.4.15.

Rubin, D.M., and McCulloch, D.S., 1979, The movement and equilibrium of bedforms in central San Francisco Bay, in Conomos, T.J., San Francisco Bay - The Urbanized Estuary: American Association for the Advancement of Science, Pacific Division, San Francisco, Calif., p. 97-114.

Rudek, J., and Cloern, J.E., 1996, Planktonic respiration rates in San Francisco Bay, in Hollibaugh, J.T., ed., San Francisco Bay – The Ecosystem: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 289-304.

Ruhl, C.A., and Schoellhamer, D.H., 1999, Time series of suspended-solids concentrations in Honker Bay during water year 1997, in 1997 Annual Report of the San Francisco Estuary Regional Monitoring Program: San Francisco Estuary Institute, p. 82-92.

Ruhl, C.A., and Schoellhamer, D.H., 2001, Time series of SSC, salinity, temperature, and total mercury concentration in San Francisco Bay during water year 1998: Regional Monitoring Program for Trace Substances contribution number 44, San Francisco Estuary Institute, Richmond, California.

Ruhl, C.A., and Schoellhamer, D.H., 2004, Spatial and Temporal Variability of Suspended-Sediment Concentrations in a Shallow Estuarine Environment: San Francisco Estuary and Watershed Science. v. 2, no. 2, article 1.

Ruhl, C.A., Schoellhamer, D.H., Stumpf, R.P., and Lindsay, C.L., 1999, Remote sensing: visual cues to suspended-solids transport in San Francisco Bay, California: Proceedings of the 4th biennial State of the Estuary Conference, San Francisco, Calif., March 17-19, 1999, p. 74.

Ruhl, C.A., Schoellhamer, D.H., Stumpf, R.P., and Lindsay, C.L., 2001, Combined use of remote sensing and continuous monitoring to analyze the variability of suspended-sediment concentrations in San Francisco Bay, California: Estuarine, Coastal and Shelf Science, v. 53, p. 801-812.

Schemel, L.E., 1971, Seasonal distributions of salinity, phytoplankton nutrients, and dissolved organic carbon in south San Francisco Bay, 1969-1970: San Jose State University, San Jose, Calif., Master's Thesis, 54 p.

Schemel, L.E., 1983, Salinity, alkalinity, dissolved and particulate organic carbon in the Sacramento River at Rio Vista, California and at other locations in the Sacramento, San Joaquin Delta: U.S. Geological Survey Water Resources Investigations Report 83-4059, 45 p.

Schemel, L.E., 1983, Seasonal patterns of alkalinity in the San Francisco Bay estuarine system, California, during 1980: U.S. Geological Survey Water Resources Investigations, 82-4102, 80 p.

Schemel, L.E., 1989, Potamocorbula Amurensis discovered in San Francisco Bay, Interagency Ecological Study Program Newsletter, v.1, n.3, p.3.

Schemel, L.E., 1995, Benthic macrofauna data for San Francisco Bay, California, September 1989: U.S. Geological Survey Open-File Report 95-291.

Schemel, L.E., 1995, Measurement of salinity, temperature, and tides in southern San Francisco Bay, California, at Dumbarton Bridge: 1990-1993 water years: U.S. Geological Survey Open-File Report 95-326 25 p. [plus appendix and 4 data disks]

Schemel, L.E., 1995, Supporting data for hydrologic studies in San Francisco Bay, California: meteorological measurements at the port of Redwood City during 1992-1994: U.S. Geological Survey Open-File Report 95-327 30 p. [plus disk]

Schemel, L.E., 1998, Effects of delta outflow and local stream flow on salinity in south San Francisco Bay: 1995-1998: Interagency Ecological Program Newsletter, v. 11, no. 4, p. 32-33.

Schemel, L.E., 1998, Salinity and temperature in south San Francisco Bay, California, at Dumbarton Bridge: measurements from the 1995-1998 water years and comparisons with results from the 1990-1993 water years: U.S. Geological Survey Open-File Report 98-650.

Schemel, L.E., 1998, Supporting data for hydrologic studies in San Francisco Bay, California: meteorological measurements at the port of Redwood City, 1995-1997: U.S. Geological Survey Open-File Report 98-64.

Schemel, L.E., 2001, Simplified conversions between specific conductance and salinity units for use with data from monitoring stations: Interagency Ecological Program Newsletter, v.14, n.1, p. 17-18.

Schemel, L.E., 2002, Supporting data for hydrologic studies in San Francisco Bay, California: Meteorological measurements at the port of Redwood City during 1998-2001, U.S. Geological Survey Open-file Report 02-231, 37p. plus data files.

Schemel, L.E., Alpine, A.E., Cole, B.E., Dedini, L.A., and Spiker, E.C., 1979, Water and sediment measurements in San Francisco Bay, California: U.S. Geological Survey Open-File Report 78-973, 28 p.

Schemel, L.E., Brown, R.L., and Bell, N.W., 2003, Salinity and temperature in south San Francisco Bay, California, at Dumbarton Bridge: Results from the 1999-2002 water years and an overview of previous data, U.S. Geological Survey Water Resources Investigations Report 03-4005, 32p. plus data files.

Schemel, L.E., Cox, M.H., Hager, S.W., and Sommer, T.R., 2002, Hydrology and chemistry of floodwaters in the Yolo Bypass, Sacramento River system, California, during 2000, U.S. Geological Survey Water Resources Investigations Report 02-4202, 65p.

Schemel, L.E., and Dedini, L.A., 1979, A continuous water-sampling and multi-parameter/measurement system for estuaries: U.S. Geological Survey Open-File Report 79-273, 28 p.

Schemel, L.E., and Dedini, L.A., 1979, Particulate organic carbon in San Francisco Bay, California, 1971-1977: U.S. Geological Survey Open-File Report 79-512.

Schemel, L.E., and Dedini, L.A., 1982, Continuous water sampling and water analysis in estuaries: U.S. Geological Survey Open-File Report 82-551, 27 p.

Schemel, L.E., and Hager, S.W., 1986, Chemical variability in the Sacramento River and in northern San Francisco Bay: Estuaries v. 9, p. 270-283.

Schemel, L.E., and Hager, S.W., 1996, Dissolved inorganic nitrogen, phosphorus, and silicon in south San Francisco Bay, II, a case study of effects of local climate and weather, in Hollibaugh, J.T., ed., San Francisco Bay: The Ecosystem: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 237-260.

Schemel, L.E., Hager, S.W., and Childers, D., 1995, The supply of suspended sediment from the Sacramento River to San Francisco Bay, I, concentrations and transports, in Hollibaugh, J.T., ed., San Francisco Bay – The Ecosystem: American Association for the Advancement of Science, Pacific Division, San Francisco, p. 217-235.

Schemel, L.E., Harmon, D.D., Hager, S.W., and Peterson, D.H., 1984, Response of northern San Francisco Bay to riverine inputs of dissolved inorganic carbon, silicon, nitrogen and phosphorus, in Kennedy, V.S., ed., The Estuary as a Filter: Academic Press, New York, p. 221-240.

Schemel, L.E., Hager, S.W., and Peterson, D.H., 1999, Reduced phosphate loading to South San Francisco Bay, California: Detection of effects in the water column. Proceedings of the Technical Meeting Charleston, SC, March 8-12, 1999, U.S. Geological Survey Water Resources Investigations Report 99-4018B, Vol. 2, p. 59-64.

Schemel, L.E., Ota, A.Y., Hager, S.W., and Swithenbank, A.M., 1989, Sources of dissolved and particulate substances to the Sacramento River near Sacramento, California, Summer, 1985: U.S. Geological Survey Open-File Report 89-45, 62 p.

Schemel, L.E., Ota, A.Y., Harmon, J.G., Shay, J.M., and Adorodor, R.N., 1988, Benthic macrofauna and ancillary data for San Francisco Bay, California, march to november 1987: U.S. Geological Survey Open-File Report 88-192, 73 p.

Schemel, L.E., Ota, A.Y., Harmon, J.G., Shay, J.M., and Adorodor, R.N., 1990, Benthic macrofauna and ancillary data for San Francisco Bay, California, January to November 1988: U.S. Geological Survey Open-File Report 89-596, 65 p.

Schemel, L.E., Sommer, T.R., Mueller-Solger, A.B., and Harrell, W.C., 2004, Hydrologic variability, water chemistry, and phytoplankton biomass in a large floodplain of the Sacramento River, CA, USA. Hydrobiologia v. 513, p. 129-139.

Schoellhamer, D.H., 1994, Central San Francisco Bay suspended-sediment transport processes study and comparison of continuous and discrete measurements of suspended-solids concentrations: San Francisco Estuary Regional Monitoring Program for Trace Substances, 1993 Annual Report, p. 129-134.

Schoellhamer, D.H., 1996, Central San Francisco Bay suspended-sediment transport processes and comparison of continuous and discrete measurements of suspended-solids concentrations: San Francisco Estuary Regional Monitoring Program for Trace Substances, 1994 Annual Report, p. 198-206.

Schoellhamer, D.H., 1996, Factors affecting suspended-solids concentrations in south San Francisco Bay, California: Journal of Geophysical Research, v. 101, no. C5, p. 12,087-12,095.

Schoellhamer, D.H., 1997, Time series of suspended-solids concentration, salinity, temperature, and total mercury concentration in San Francisco Bay during water year 1996: 1996 Annual Report of the Regional Monitoring Program for Trace Substances, p. 65-77.

Schoellhamer, D.H., 1997, Time series of trace element concentrations calculated from time series of suspended-solids concentrations and RMP water samples: 1995 Annual Report of the Regional Monitoring Program for Trace Substances, p. 53-55.

Schoellhamer, D.H, 2001, Influence of salinity, bottom topography, and tides on locations of estuarine turbidity maxima in northern San Francisco Bay, in McAnally, W.H., and Mehta, A.J., ed., Coastal and Estuarine Fine Sediment Transport Processes: Elsevier Science B.V., p. 343-357.

Schoellhamer, D.H., 2001, Singular spectrum analysis for time series with missing data: Geophysical Research Letters, v. 28, no. 16, p. 3187-3190.

Schoellhamer, D.H., 2002, Comparison of basin-wide effect of dredging and natural estuarine processes on suspended-sediment concentration: Estuaries, v. 25, no. 3, p. 488-495.

Schoellhamer, D.H., 2002, Variability of suspended-sediment concentration at tidal to annual time scales in San Francisco Bay, USA: Continental Shelf Research, v. 22, p. 1857-1866.

Schoellhamer, D.H., and Burau, J.R., 1998, Summary of findings about circulation and the estuarine turbidity maximum in Suisun Bay, California: U.S. Geological Survey Fact Sheet FS-047-98, 6 p.

Schoellhamer, D.H., and Warner, J.C., 2001, A turbidity maximum and flood/ebb asymmetry of suspended sediment: Proceedings of the 5th biennial State of the Estuary Conference, San Francisco, Calif., October 9-11, 2001, p. 33.

Schoellhamer, D.H., and Wright, S.A., 2002, Continuous monitoring of suspended sediment in rivers by use of optical backscatterance sensors: Proceedings of the IAHS workshop on Erosion and sediment transport measurement: Technological and Methodological advances, Oslo, Norway, June 19-21, 2002.

Schoellhamer, D.H., and Wright, S.A., 2003, Continuous monitoring of suspended sediment discharge in rivers by use of optical backscatterance sensors, in Bogen, J., Fergus, T., and Walling, D.E., ed., Erosion and Sediment Transport Measurement: Technological and Methodological Advances: International Association for Hydrological Science Publication 283, p. 28-36.

Schoellhamer, D.H., Buchanan, P.A., and Ganju, N.K., 2002, Ten years of continuous suspended-sediment concentration monitoring in San Francisco Bay and Delta: Proceedings of the Turbidity and Other Sediment Surrogates Workshop, Reno, Nevada, April 30 - May 2, 2002.

Schoellhamer, D.H., Ganju, N.K., Gartner, J.W., Murrell, M.C., and Wright, S.A., 2003, Seasonal and longitudinal homogeneity of suspended sediment in San Francisco Bay, California: Proceedings of the 17th Biennial Conference of the Estuarine Research Federation, Seattle, Washington, September 14-18, 2003, p. 119.

Schoellhamer, D.H., Lionberger, M.A., Jaffe, B.E., Ganju, N.K., Wright, S.A., and Shellenbarger, G.G., 2005, Bay Sediment Budgets: Sediment Accounting 101: The Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary, San Francisco Estuary Institute, Oakland, California, p. 58-63.

Schoellhamer, D.H., Oltmann, R.N., Jaffe, B.E., and Smith, R.E.,1996, Sediment supply and wetlands in San Francisco Bay, in 3rd Biennial State of the Estuary Conference, October 10, 11, 12, 1996, Officers Club, Presidio of San Francisco: [Oakland, Calif., San Francisco Estuary Project], Abstract book, p. 23.

Schoellhamer, D.H., Orlando, J.L., Wright, S.A., and Freeman, L.A., 2006, Sediment supply and demand: Proceedings of the South Bay Science Symposium, June 6, 2006, San Jose, California, p. 3.

Schoellhamer, D.H., Shellenbarger, G.G., Ganju, N.K., Davis, J.A., and McKee, L.J., 2003, Sediment dynamics drive contaminant dynamics: The Pulse of the Estuary: Monitoring and Managing Contamination in the San Francisco Estuary, San Francisco Estuary Institute, Oakland, California, p. 21-26.

Shellenbarger, G.G., and Boehm, A.B., 2005, Potential degradation of water quality by bird feces in and around managed wetlands: Proceedings of the 7th biennial State-of-the-Estuary Conference, Oakland, California, October 4-6, 2005, p. 174.

Shellenbarger, G.G., and Boehm, A.B., 2006, Degradation of water quality by bird feces in and around managed wetlands: Proceedings of the South Bay Science Symposium, June 6, 2006, San Jose, California, p. 19.

Shellenbarger, G.G., Schoellhamer, D.H., and Lionberger, M.A., 2004, A South San Francisco Bay Sediment Budget: Wetland Restoration and Potential Effects on Phytoplankton Blooms: Proceedings of the 2004 Ocean Research Conference, Honolulu, Hawaii, February 15-20, 2004.

Shouse, M.K., 2002, The effects of decreasing trace metal concentrations on benthic community structure, M.A. Thesis, San Francisco State University, 177 p.

Shouse, M.K, Parchaso, F., and Thompson, J.K., 2003, Near-field receiving water monitoring of a benthic community near the Palo Alto water quality control plant in south San Francisco Bay: February 1974 through December 2000: U.S. Geological Survey Open-File Report 03-224.

Shouse, M.K, Parchaso, F., and Thompson, J.K., 2004, Near-field receiving water monitoring of a benthic community near the Palo Alto water quality control plant in south San Francisco Bay: February 1974 through December 2003: U.S. Geological Survey Open-File Report 2004-1210.

Simpson, J.J., Dettinger, M.D., Gerhke, F., McIntyre, T.J., and Hufford, G.I., 2004, Hydrologic scales, cloud variability, remote sensing and models—Implications for forecasting snowmelt and streamflow: Weather and Forecasting, 19, 251-276.

Simpson, M.R., and Oltmann, R.N., 1993, Discharge-measurement system using an acoustic doppler current profiler with applications to large rivers and estuaries: U.S. Geological Survey Water-Supply Paper 2395, 32 p.

Slack, J.R., and Landwehr, J.M., 1992, Hydro-climatic data network: a U.S. Geological Survey discharge data set for the United States for the study of climate variations during the last century, 1874-1988: U.S. Geological Survey Open-File Report 92-129, 193 p.

Smalling, K.L., Orlando, J.L., and Kuivila, K.M., 2005, Analysis of Pesticides in Surface Water and Sediment from Yolo Bypass, California, 2004–2005: U.S. Geological Survey Scientific Investigations Report 2005-5220, 20 p.

Smetacek, V. and Cloern, J.E., 2008, Oceans: On phytoplankton trends. Science, v. 319 (5868):1346-1348

Smith, L.H., 1987, A review of circulation and mixing studies of San Francisco Bay, California: U.S. Geological Survey Circular 1015, 38 p.

Smith, L.H., and Cheng, R.T., 1976, Tidal stream flow solved by Galerkin technique, in Proceedings of the 15th Coastal Engineers Conference, Honolulu, Hawaii, p. 3,358-3,376.

Smith, L.H., and Cheng, R.T., 1987, Tidal and tidally averaged circulation characteristics of Suisun Bay, California: Water Resources Research, v. 23, p. 143-155.

Smith, P.E., 1994, San Francisco Bay test case for 3-D model verification, in Proceedings of the 1994 National Conference on Hydraulic Engineering, Buffalo, N.Y., August 1-5, 1994: American Society of Civil Engineers, v. 2, p. 885-889.

Smith, P.E., and Cheng, R.T., 1989, Recent progress on hydrodynamic modeling of San Francisco Bay, California, in Estuarine and Coastal Modeling: American Society of Civil Engineers, University of Rhode Island, Kingston, R.I., p. 502-510.

Smith, P.E., and Cheng, R.T., 1990, Recent progress on hydrodynamic modeling of San Francisco Bay, California: in Proceedings of Conference on Estuarine and Coastal Circulation and Pollutant Transport Modeling, Newport, R.I., November 15-17, 1989, p. 502-510.

Smith, P.E., and Larock, B.E., 1993, A finite-difference model for 3-D flows in bays and estuaries, in Proceedings of the 1993 National Conference on Hydraulic Engineering, San Francisco, Calif., July 25-30, 1993: American Society of Civil Engineers, 6 p.

Smith, P.E., Cheng, R.T., Burau, J.R., and Simpson, M.R., 1991, Gravitational circulation in a tidal strait: in Proceedings of the 1991 National Conference on Hydraulic Engineering, Nashville, Tenn., July 29-August 2, 1991: American Society of Civil Engineers, p. 429-434.

Smith, P.E., Oltmann, R.N., and Simpson, M.R., 1992, Data set for verification of 3-D free-surface hydrodynamic models, Carquinez Strait, California: American Society of Civil Engineers, Proceedings of the Hydraulic Engineering Sessions Water Forum 1992, Baltimore, Md., August 2-6, p. 430-435.

Smith, P.E., Oltmann, R.N., and Smith, L.H., 1995, Summary report on the interagency hydrodynamic study of San Francisco Bay-Delta estuary, California: Interagency Ecological Program for the Sacramento–San Joaquin Estuary, Technical Report 45, 72 p.

Smith, R.E., Foxgrover, A., and Jaffe, B.E., 2003, Suisun Bay and Delta Bathymetry production of a 10-meter grid, Second Biennial CALFED Science Conference, Poster and Web site.

Smith, R.E., Herndon, R.E., and Harmon, D.D., 1979, Physical and chemical properties of San Francisco Bay waters, 1969-1976: U.S. Geological Survey Open-File Report 79-511, 607 p.

Smith, R.E., Jaffe, B., Torresan, L.Z., Malzone, C., Capiella, K., Leech, R., Carbon, S., and Foxgrover, A., 2002, San Francisco Bay bathymetry Web site, U.S. Geological Survey, Coastal and Marine Geology Program.

Smith, R.E., Peterson, D.H., Hager, S.W., Harmon, D.D., Schemel, L.E., and Herndon, R.E., 1985, Seasonal and interannual nutrient variability in northern San Francisco Bay, in Sigleo, A., ed., Marine and Estuarine Geochemistry: American Chemical Society, p. 137-159.

Smith, R.L., and Oremland, R.S., 1983, Anaerobic oxalate degradation: Widespread natural occurrence in aquatic sediments: Applied and Environmental Microbiology, v. 46, p. 106-113.

Smith, R.L., and Oremland, R.S., 1987, Big Soda Lake (Nevada), 2, pelagic sulfate reduction: American Society of Limnology and Oceanography, v. 32, no. 4, p. 794-803.

Sobczak, W.S., Cloern, J.E., Jassby, A.D., and Mueller-Solger, A., 2002, Bioavailability of organic matter in a highly disturbed estuary: the role of detrital and algal resources: Proceedings of the National Academy of Sciences, v. 99, p. 8,101-8,105.

Sobczak, W.S., Cloern, J.E., Jassby, A.D., Cole, B.E., Schraga, T.S., Arnsberg, A., 2005, Detritus Fuels Ecosystem Metabolism but not Metazoan Food Webs in San Francisco Estuary's Freshwater Delta, Estuaries 28: 122-135.

Sommer, T., Harrell, B., Nobriga, M., Brown, R., Moyle, P., Kimmerer, W., and Schemel, L., 2001, California's Yolo Bypass: Evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture, Fisheries, v.26, n.8, p.6-16.

Spiker, E.C., 1980, The behavior of 14-C and 13-C in estuarine water: effects of in situ CO production and atmospheric exchange: Radiocarbon, v. 22, p. 647-654.

Spiker, E.C., and Schemel, L.E., 1979, Distribution and stable-isotope composition of carbon in San Francisco Bay, in Conomos, T.J., ed., San Francisco Bay, the Urbanized Estuary: American Association for the Advancement of Science, p. 195-212.

Stacey, M.T., Monismith, S.G., and Burau, J.R., 1999, Measurements of Reynolds stress profiles in unstratified tidal flow: Journal of Geophysical Research, v. 104, no. C5, p. 10,933-10,949.

Stacey P.E., Greening, H., Kremer, J.N., Peterson, D., and Tomasko, D., 2001, Contributions of Atmospheric Nitrogen Deposition to U.S. Estuaries: Summary and Conclusions, in Valigura, R.A., and others, eds., Nitrogen Loading in Coastal Water Bodies: An atmospheric perspective: American Geophysical Union, p. 187-226

Stahle, D.W., Therrell, M.D., Cleaveland, M.K., Cayan, D.R., Dettinger, M.D., and Knowles, N., 2001, Ancient blue oaks reveal human impact on San Francisco Bay salinity: American Geophysical Union, v. 82, no. 12, p. 141, 144-145

Starner, K., Kuivila, K.M., Jennings, B., and Moon, G.E., 1999, Degradation rates of six pesticides in water from the Sacramento River, California, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2 of 3—Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 89-98.

Sternberg, R.W., Cacchione, D.A., Drake, D.E., and Kranck, K., 1986, Suspended sediment dynamics in an estuarine tidal channel in San Francisco Bay, California: Marine Geology, v. 71, p. 237-258.

Sternberg, R.W., Johnson, R.V. II, Cacchione, D.A., and Drake, D.E., 1986, An instrument system for monitoring and sampling suspended sediment in the benthic boundary layer: Marine Geology, v. 71, p. 187-199.

Sternberg, R.W., Kranck, K., Cacchione, D.A., and Drake, D.E., 1988, Suspended sediment transport under estuarine tidal channel conditions: Dedimentry Geology, v. 57, p. 257-272.

Stewart, A.R., Luoma, S.N., Schlekat, C.E., Doblin, M.A., and Hieb, K.A., 2004, Food Web pathway Determines How Selenium Affects Aquatic Ecosystems: A San Francisco Bay Case Study, Environmental Science and Technology, v. 38, no. 17, p. 4519-4526.

Stewart, I., Cayan, D.R., and Dettinger, M.D., 2004, Changes in snowmelt runoff timing in western North America under a business as usual climate change scenario: Climatic Change, v. 62, 15 p.

Strong, C.R., and Luoma, S.N., 1981, Variations in correlation of body size with concentrations of Cu and Ag in bivalve Macoma balthica: Canadian Journal of Fisheries and Aquatic Science, v. 38 no. 9, p. 1,059-1,064.

Swanson, K.M., Shellenbarger, G., Henderson, K., DiLeo, J.S., Schoellhamer, D.H., 2004, Science Support for Salt Pond Restoration and Management in South San Francisco Bay: U.S. Geological Survey Fact Sheet 2004-3135, 4 p.

Swanson, K.M., Shellenbarger, G.G., Henderson, K.D., DiLeo, J.S., Schoellhamer, D.H., Takekawa, J.Y., Athearn, N.D., Jaffe, B.E., Miles, A.K., Saiki, M.K., and Lionberger, M.A., 2004, Science support for salt pond restoration and management in South San Francisco Bay: U.S. Geological Survey Fact Sheet 2004-3135, 4 p.

Swanson, K.M., Shellenbarger, G.G., Schoellhamer, D.H., Ganju, N. K., Athearn, N., and Buchanan, P., 2003, Desalinization, erosion, and tidal changes following the breaching of Napa salt pond 3: Proceedings of the 6th biennial State-of-the-Estuary Conference, Oakland, California, October 21-23, 2003, p. 156.

Takekawa, J. Y., Athearn, N.D., Miles, A.K., Spring, S.E., Saiki, F.. Mejia, Woo, I., Schultz, A.K., and Hattenbach, B., 2006,  Habitat Restoration Monitoring for the Napa-Sonoma Marshes Restoration Project,  Unpublished Final Progress Report, U.S. Geological Survey, Vallejo, CA. 114p.

Takekawa, J., Demers, S., Woo, I., Athearn, N., Ganju, N., Shellenbarger, G., Schoellhamer, D., and Perry, W.M., 2003, A bathymetry system for measuring sediment accumulation in tidal marsh restoration projects: Proceedings of the 6th biennial State-of-the-Estuary Conference, Oakland, California, October 21-23, 2003, p. 157.

Takekawa, J.Y., Lu, C.T., and Pratt, R.T., 2001, Avian communities in baylands and artificial salt evaporation ponds of the San Francisco Bay estuary: Hydrobiologia, v. 466, p. 317-328.

Takekawa, J. Y., Miles, A.K., Athearn, N.D., Spring, S.E., Saiki, M.K., Mejia, F., Woo, I., and Goodenough, K.S., 2005, Habitat Restoration Monitoring for the Napa-Sonoma Marsh Restoration Project, Progress Report 2005, Unpublished Progress Report, U.S. Geological Survey, Vallejo, CA. 78p.

Takekawa, J.Y., Miles, A.K., Schoellhamer, D.H., Athearn, N.D., Saiki, M.K., Duffy, W.D., Kleinschmidt, S., Shellenbarger, G.G., and Jannusch, C.A., 2006, Trophic structure and avian communities across a salinity gradient in evaporation ponds of the San Francisco Bay estuary: Hydrobiologia, v. 567, p. 307-327.

Takekawa, J.Y., Miles, A.K., Schoellhamer, D.H., Jaffe, B., Athearn, N.D., Spring, Shellenbarger, G.G., Saiki, M.K., Mejia, F., and  Lionberger, M.A., 2005, South Bay Salt Ponds Restoration Project Short-term Data Needs, 2003-2005,  Unpublished Final Report, U.S. Geological Survey, Vallejo, CA. 270 p.

Takekawa, J.Y., Miles, A.K., Schoellhamer, D.H., Martinelli, G., Saiki, M.K., and Duffy, W.G., 2001, Science support for wetland restoration in the Napa-Sonoma salt ponds, San Francisco Bay estuary, 2000 progress report, Unpublished Progress Report: U.S. Geological Survey, Davis and Vallejo, Calif., 66 p.

Takekawa, J. Y., Schoellhamer,D.H., Miles, A.K., Shellenbarger, G.G., Athearn, N.D., Spring, S.E., Saiki, M.K., and Jannusch, C.A.,  2004,  Initial biophysical changes after breaching a salt pond levee: final report on the Napa-Sonoma Wildlife Area Pond 3 breach.  Unpublished Progress Report, U.S. Geological Survey, Vallejo, CA.  42p.

Takekawa, J.Y., Warnock, N., Martinelli, G., Miles, A.K., and Tsao, D., 2002, Waterbird use of bayland wetlands in the San Francisco Bay estuary: movements of long-billed dowitchers during the winter: Waterbirds, v. 25, p. 93-105.

Taylor, M.J., and Yost, B.T., 1990, Description of salinity, temperature, chlorophyll, suspended sediment, and velocity data, south San Francisco Bay, California, February-April, 1987: U.S. Geological Survey Open-File Report 89-619, 28 p.

Teh, S.J., Clark, S.L., Brown, C.L., Luoma, S.N., and Hinton, D.E., 1999, Enzymatic and histopathilogic biomarkers as indicators of contaminant exposure and effect in asian clam (Potamocorbula amurensis): Biomarkers, v. 4, p. 497–509.

Thébault, J., Schraga, T.S., Cloern, J.E., and Dunlavey, E.G., 2008, Primary Production and Carrying Capacity of Former Salt Ponds After Reconnection to San Francisco Bay. Wetlands, vol. 28, p. 841-851.

Thompson, J.K., 1979, Population dynamics and sediment relations of Gemma gemma in San Francisco Bay: San Francisco State University, San Francisco, Calif., Master's Thesis.

Thompson, J.K., 1982, Population dynamics and sediment relations of Gemma gemma in south San Francisco Bay, with a comparison to some north-eastern United States estuarine populations: Veliger, v. 24, p. 281-290.

Thompson, J.K., 1999, The effect of infaunal bivalve grazing on phytoplankton bloom development in south San Francisco Bay: Stanford University, Stanford, Calif., Ph.D. dissertation, 419 p.

Thompson, J.K., 2002, The evolving benthic community, in Science and strategies for restoration: San Francisco Estuary Project Editors, p. 66-67.

Thompson, J.K., 2005, One estuary, one invasion, two responses: phytoplankton and benthic community dynamics determine the effect of an estuarine invasive suspension-feeder, in The Comparative roles of Suspension-Feeders in Ecosystems.  R.F. Dame and S. Olenin (eds),  P. 291-316.

Thompson, J.K., and Nichols, F.H., 1981, Benthic macrofaunal biomass of San Francisco Bay, California: January, February and August, 1973: U.S. Geological Survey Open-File Report 81-1331, 39 p.

Thompson, J.K., and Nichols, F.H., 1984, Benthic macrofauna of a south San Francisco Bay, California, mud flat, 1974 to 1983: U.S. Geological Survey Open-File Report p. 84-759, 200 p.

Thompson, J.K., and Nichols, F.H., 1988, Food availability controls the seasonal cycle of growth in the bivalve Macoma balthica: Journal of Experimental Marine Biology and Ecology, v. 116, p. 43-61.

Thompson, J.K., Nichols, F.H., and Wienke, S.M., 1981, Distribution of benthic chlorophyll in San Francisco Bay, California, February, 1980-February, 1981: U.S. Geological Survey Open-File Report 81-1134, 36 p.

Thompson, J.K., Parchaso, F., and Shouse, M.K., 2002, Near-field receiving water monitoring of a benthic community near the Palo Alto water quality control plant in south San Francisco Bay: February 1974 through December 2002: U.S. Geological Survey Open-File Report 02-394.

Thompson, J.K., Parchaso, F., Brown, C.L., and Luoma, L.N., 1996, In situ ecosystem effects of trace contaminants in the San Francisco Bay estuary: the necessary link to establishing water quality standards: U.S. Geological Survey Open-File Report 96-437.

Thompson, J.K., Stewart, A.R., and Parchaso, F., 2001, Behind the energetics of the asiatic clam, Potamocorbula amurensis, in San Francisco Bay: Interagency Ecological Program for the San Francisco Estuary Newsletter, v. 14, no. 4, p. 30.

Thompson, J.K., 1997, Impacts of the Asian Clam on San Francisco Bay, California: Proceedings of the Meeting of the American Fisheries Society, Monterey, Calif., 1997.

Thomson, E.A., Luoma, S.N., Johansson, C.E., and Cain, D.J., 1984, Comparison of sediments and organisms in identifying sources of biologically available trace metal contamination: Water Resources, v. 18, no. 6, p. 755-765.

Thomson-Becker, E.A., and Luoma, S.N., 1985, Temporal fluctuations in grain size, organic materials and iron concentrations in intertidal surface sediment of San Francisco Bay: Hydrobiologia, v. 129, p. 91-108.

Tobin, A., Schoellhamer, D.H., and Burau, J.R., 1995, Suspended-solids flux in Suisun Bay, Cali fornia: Proceedings of the First International Conference on Water Resources Engineering, San Antonio, Tex., August 14-18, 1995, v. 2, p. 1,511-1,515.

Topping, B.R., and Kuwabara, J.S., 1999, Flow-injection-ICP-MS method applied to benthic flux studies of San Francisco Bay, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program—Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999, v. 2— Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 131-134.

Topping, B.R., J.S. Kuwabara, M.C. Marvin-Dipasquale, J.L. Agee, L.H. Kieu, J.R. Flandro, F. Parchaso, S.W. Hager, C.B. Lopez, D.O. Krabbenhoft. 2004.  Sediment remobilization of mercury in South San Francisco Bay, California.  U.S.G.S. Scientific Investigation Report 2004-5196.  (http://pubs.water.usgs.gov/sir2004-5196).

Topping, B.R., Kuwabara, J.S., Parchaso, F., Hager, S.W., Arnsberg, A.J., Murphy, F., 2001, Benthic Flux of Dissolved Nickel in the Water Column of South San Francisco Bay: U.S. Geological Survey Open-File Report 01-089, 50 p. (abstract or to obtain pdf file)

Uncles, R.J., and Peterson, D.H., 1993, Modeling the long-term salinity field in San Francisco Bay: submitted to Water Resources Research.

Uncles, R.J., and Peterson, D.H. 1995, A computer model of long-term salinity in San Francisco Bay: sensitivity to mixing and inflows: Environmental International, v. 21, p. 647-656.

Uncles, R.J., and Peterson, D.H., 1996, The long-term salinity field in San Francisco Bay: Continental Shelf Research, v. 16, no. 15, p. 2,005-2,039.

Uncles, R.J., Peterson, D.H., and Cayan, D.R., 1994, Prediction of long-term salinity in San Francisco Bay during drought conditions, in proceedings of an International Society of Geographer and Engineers, Dehi, India, 15 p.

Van Geen, A., and Luoma, S.N., 1993, Trace metals Cd, Cu, Ni, Zn, and nutrients in coastal waters adjacent to San Francisco Bay, California: Estuaries, v. 16, no. 3A, p. 559-566.

Van Geen, A., and Luoma, S.N., 1999, A record of estuarine water contamination from the Cd content of foraminifera tests in San Francisco Bay, California: Marine Chemistry, v. 64, nos. 1 &  2, p. 57-69.

Van Geen, A., and Luoma, S.N., 1999, The impact of human activities on sediments of San Francisco Bay, California – an overview: Marine Chemistry, v. 64, nos. 1 & 2, p. 1-6.

Van Geen, A., Luoma, S.N., Fuller, C.C., Anima, C.C.R., Clifton, H.E., and Trumbore, S., 1992, Evidence from Cd/Ca ratios in foraminifera for greater upwelling off California 4,000 years ago: Nature, v. 358, p. 54-56.

Van Geen, A., Valette-Silver, N.J., Luoma, S.N., Fuller, C.C., Baskaran, M., Tera, F., and Klein, J., 1999, Constraints on the sedimentation history of San Francisco Bay from ¹⁴C and ¹⁰Be: Marine Chemistry, v. 64, nos. 1 & 2, p. 29-38.

Vayssieres, M. and Peterson, H., 2003, Cross-channel variability in benthic habitat, Interagency Ecological Program Newsletter, 16(2):51-56.

Venkatesan, M.I., de Leon, R.P., van Geen, A., and Luoma, S.N., 1999, Chlorinated hydrocarbon pesticides and polychlorinated biphenyls in sediment cores from San Francisco Bay: Marine Chemistry, v. 64, nos. 1 & 2, p. 85-97.

Vogel, T.M., Oremland, R.S., and Kvenvolden, K.A., 1982, Low temperature formation of hydrocarbon gases in San Francisco Bay sediment: Chemical Geology, v. 37, p. 91-108.

Walters, R.A., 1981, Experiences with the application of the finite element method to the solution of the shallow water equations, in Proceedings of the Seminar on two-dimensional flow modeling: U.S. Army Corps of Engineers, Hydrologic Engineeering Center, Davis, Calif.

Walters, R.A., 1982, Low-frequency variations in sea level and currents in south San Francisco Bay: Journal of Physical Oceanography, v. 12, p. 658-668.

Walters, R.A., 1983, Time and tide: A harmonic and finite element approximation, in Proceedings of the Fifth International Conference on Finite Elements in Flow Problems, 4 p.

Walters, R.A., 1984, Finite element solution methods for circulation in estuaries, Proceedings, Fifth International Conference on Finite Elements in Water Resources, University of Vermont, Burlington, Vermont, p. 587-596.

Walters, R.A., and Cheng, R.T., 1979, A two-dimensional hydrodynamic model of a tidal estuary: Advances in Water Resources, v. 2, p. 117-184.

Walters, R.A., and Cheng, R.T., 1980, Accuracy of an estuarine hydro-dynamic model using smooth elements: Water Resources Research, v. 16, no. 1, p. 187-195.

Walters, R.A., and Cheng, R.T., 1980, Calculation of estuarine residual currents using the finite element method: Third International Conference on Finite Elements in Flow Problems, v. 2, p. 6-69.

Walters, R.A., and Gartner, J.W., 1985, Sub-tidal sea level and current variations in the northern reach of San Francisco Bay: Estuarine, Coastal and Shelf Science, v. 21, p. 17-32.

Walters, R.A., and Heston, C., 1982, Notes and correspondence: removing tidal-period variations from time-series data using low-pass digital filters: Journal of Physical Oceanography, v. 12, p. 658-668.

Walters, R.A., Cheng, R.T., and Conomos, T.J., 1985, Time scales of circulation and mixing processes of San Francisco Bay waters: Hydrobiologia, v. 129, p. 13-36.

Wang, J., and Cheng, R.T., 1990, Predicting the vertical structure of tidal current salinity in San Francisco Bay, California: Water Resources Research, v. 26, p. 1,027-1,045.

Wang, J., and Cheng, R.T., 1993, On low-pass digital filters in oceanography: Acta Oceanologics, v. 12, no. 2, p. 183-196.

Wang, J., Cheng, R.T., and Smith, P.C., 1997, Seasonal sea-level variations in San Francisco Bay in response to atmospheric forcing, 1980: Estuarine, Coastal and Shelf Science, v. 45, p. 39-52.

Wang, P.F., Cheng, R.T., Richter, K., Gross, E.S., and Gartner, J.W., 1998, Modeling tidal hydrodynamics of San Diego Bay, California: Journal of the American Water Resources Association, v. 34, no. 5, p. 1,123-1,140.

Wang, W-X., Fisher, N.S., and Luoma, S.N., 1995, Assimilation of trace elements ingested by the mussel Mytilus edulis: effects of algal food abundance: Marine Ecology Progress Series, v. 129, p. 165-176.

Wang, W-X., Fisher, N.S., and Luoma, S.N., 1996, Kinetic determinations of trace element bioaccumulation in the mussel Mytilus edulis: Marine Ecology Progress Series, v. 140, p. 91-113.

Warner, J.C., Schladow, S.G., and Schoellhamer, D.H., 1999, Summary and analysis, hydrodynamic and water-quality data for the Napa/Sonoma marsh complex, final report: University of California, Davis, Department of Civil and Environmental Engineering.

Warner, J.C., Schoellhamer, D.H., and Burau, J.R., 1997, A sediment transport pathway in the back of a nearly semienclosed subembayment of San Francisco Bay, California: Proceedings, XXVII International Association of Hydraulic Research Congress, August 10-15, 1997, San Francisco, Calif., v. 2, p. 1,096-1,101.

Warner, J.C., Schoellhamer, D.H., Burau, J.R., and Schladow, S.G., 2002, Effects of Tidal Current Phase at the Junction of Two Straits: Continental Shelf Research, v. 22, p. 1629-1642.

Warner, J.C., Schoellhamer, D.H., Burau, J.R., and Schladow, S.G., 2006, Flow Convergence Caused by a Salinity Minimum in a Tidal Channel: San Francisco Estuary and Watershed Science, v. 4, no. 3.

Warner, J.C., Schoellhamer, D.H., and Schladow, G.S., 2003, Tidal truncation and barotropic convergence in a channel network tidally driven from opposing entrances: Estuarine, Coastal and Shelf Science, v. 56, p. 629-639.

Warner, J.C., Schoellhamer, D.H., Ruhl, C.A., and Burau, J.R., 2004, Floodtide pulses after low tides in shallow subembayments adjacent to deep channels: Estuarine, Coastal and Shelf Science, v. 60, no. 2, p. 213-228.

Warner, J.C., Schoellhamer, D.H., Schladow, S.G., and Burau, J.R., 1999, Napa/Sonoma marsh hydrodynamic and water-quality study: Proceedings of the 4th biennial State of the Estuary Conference, San Francisco, Calif., March 17-19, 1999, p. 126.

Warnock, N., Bishop, M.A., and Takekawa, J.Y., 2002, Spring Shorebird Migration from Mexico to Alaska: Final Report 2002, Unpublished Progress Report, Point Reyes Bird Observatory, Stinson Beach, CA, and U.S. Geological Survey, Vallejo, CA, 22p.

Warnock, N., Bishop, M.A., Takekawa, J.Y., and Williams, T.D., 2004, Pacific Flyway Shorebird Migration Program: Spring Western Sandpiper migration, Northern Baja California, Mexico to Alaska - Final Report 2004, Unpublished Progress Report, PRBO Conservation Science, Stinson Beach, CA; Prince William Sound Science Center, Cordova, AK; U.S. Geological Survey, Vallejo, CA; and Simon Fraser University, Burnaby, BC

Warnock, N., Page, G.W., Ruhlen, T.D., Nur, N., Takekawa, J.Y., and Hanson, J.T., 2002, Management and conservation of San Francisco Bay salt ponds: effects of pond salinity, area, tide, and season on Pacific flyway waterbirds: Waterbirds, v. 25, p. 79-92.

Westerling, A.L., Hidalgo, H.G., Cayan, D.R., and Swetnam, T.W., 2006, Warming and Earlier Spring Increase Western U.S. Forest Wildfire Activity. Science, v. 313, p. 940-943.

Wienke, S.M., and Cloern, J.E., 1987, The phytoplankton component of seston in San Francisco Bay: Netherlands Journal of Sea Research, v. 21, no. 1, p. 25-33.

Wienke, S.M., Alpine, A.E., Cloern, J.E., and Cole, B.E., 1990, Plankton studies in San Francisco Bay, X, chlorophyll distributions and hydrographic properties in San Francisco Bay, 1987: U.S. Geological Survey Open-File Report 90-145, 50 p.

Wienke, S.M., Cloern, J.E., and Cole, B.E., 1990, Plankton studies in San Francisco Bay, XI, chlorophyll distributions and hydrographic properties in San Francisco Bay, 1988-1989: U.S. Geological Survey Open-File Report 90-562, 212 p.

Wienke, S.M., Cole, B.E., Cloern, J.E., and Alpine, A.E., 1991, Plankton studies in San Francisco Bay, XII, chlorophyll distributions and hydrographic properties in San Francisco Bay, 1990: U.S. Geological Survey Open-File Report 91-476, 85 p.

Wienke, S.M., Cole, B.E., Cloern, J.E., and Alpine, A.E., 1992, Plankton studies in San Francisco Bay, XIII, chlorophyll distributions and hydrographic properties in San Francisco Bay, 1991: U.S. Geological Survey Open-File Report 92-158, 116 p.

Wienke, S.M., Cole, B.E., Cloern, J.E., and Alpine, A.E., 1993, Plankton studies in San Francisco Bay, XIV, chlorophyll distributions and hydrographic properties in San Francisco Bay, 1992: U.S. Geological Survey Open-File Report 93-423, 175 p.

Wilby, R.L., and Dettinger, M.D., 2000, Streamflow changes in the Sierra Nevada, California, simulated using a statistically downscaled general circulation model scenario of climate change, in McLaren, S., and Kniveton, D., eds., Linking Climate Change to Land Surface Change: Kluwer Academic Publishers, Netherlands, p. 1-20.

Wong, F.N., and Cheng, R.T., 1989, A branched hydrodynamic model of the Sacramento–San Joaquin Delta, California: Proceedings, National Conference on Hydraulic Engineering/Hydraulics Division/American Society of Civil Engineers in Hydraulic Engineering, New Orleans, La., p. 493-498.

Wong, R.L.J., and Cloern, J.E., 1981, Plankton studies in San Francisco Bay, II, phytoplankton abundance and species composition, July 1972–December 1979: U.S. Geological Survey Open-File Report, 81-214, 103 p.

Wong, R.L.J., and Cloern, J.E., 1982, Plankton studies in San Francisco Bay, IV, phytoplankton abundance and species composition, January 1980–February 1981: U.S. Geological Survey Open-File Report 82-443, 152 p.

Wood, T.M., Baptista, A.M., Kuwabara, J.S., and Flegal, A.R., 1995, Diagnostic modeling of trace metal partitioning in south San Francisco Bay: Limnology and Oceanography, v. 40, no. 2, p. 345-358.

Wright, S.A. and Schoellhamer, D.H., 2003, Trends in the sediment yield of the Sacramento River, 1957-2001: Proceedings of the 2003 CALFED Science Conference, Sacramento, California, January 14-16, 2003, p. 177.

Wright, S.A., and Schoellhamer, D.H., 2004, Suspended sediment transport where rivers become estuaries: Sacramento – San Joaquin River Delta, water years 1999-2002: Proceedings of the 2004 CALFED Science Conference, Sacramento, California, October 4-6, 2004, p. 237.

Wright, S.A., and Schoellhamer, D.H., 2004, Suspended sediment transport where rivers become estuaries: Sacramento – San Joaquin River Delta, water years 1999-2002: Eos Transactions AGU, v. 85, no. 47, Fall Meeting Supplement, Abstract H53C-1262.

Wright, S.A., and Schoellhamer, D.H., 2004, Trends in the Sediment Yield of the Sacramento River, California, 1957 – 2001: San Francisco Estuary and Watershed Science. v. 2, no. 2, article 2.

Wright, S.A., and Schoellhamer, D.H., 2005, Estimating sediment budgets at the interface between rivers and estuaries with application to the Sacramento–San Joaquin River Delta, Water Resources. Research, v. 41, W09428, doi:10.1029/2004WR003753.

Zehr, J.P., and Oremland, R.S., 1987, Reduction of selenate to selenide by sulfate-respiring bacteria: experiments with cell suspensions and estuarine sediments: Applied and Environmental Microbiology, v. 53, no. 6, p. 1,365-1,369.

Zehr, J.P., Harvey, R.W., Oremland, R.S., Cloern, J.E., George, L.H., and Lane, J.L., 1987, Big Soda Lake (Nevada), 1, pelagic bacterial heterotrophy and biomass: American Society of Limnology and Oceanography, v. 32, no. 4, p. 781-793.