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Transient Storage Reader 2

The Transient Storage Concept --
Comprehensive Readings on Applications for Stream Solute Transport with Selected References in the Context of Stream-Catchment Connections, Hyporheic Exchange Flows, and Reactive Solute Transport

Compilation by Ken Bencala <kbencala@usgs.gov>
original: October 1997
revised: 01-Jun-1998, 15-Feb-1999, 15-Sep-1999, 23-Feb-2000, 23-Aug-2000, 18-Feb-2001, 7-Nov-2001
last update: 20-May-2005

This reading list also may be downloaded as a Word document [111 kB].

Transient Storage Reader 2 presents a comprehensive reference list of application, analysis, and development of the transient storage concept, specifically as implemented in the OTIS/OTEQ model packages. The list additionally includes selected references in the context of stream-catchment connections, hyporheic exchange flows and reactive solute transport in streams, specifically as such references provide insights to implementation and interpretation of OTIS/OTEQ applications.

For essential references for starting an application of the transient storage concept, specifically as implemented in the OTIS model package, see Transient Storage Reader 1.

For any application, the USGS Fact Sheet on Using OTIS illustrates the concepts of the transport model. Comprehensive chapters in Streams and Ground Waters include thoughtful discussions relating the idealized transient storage concept to the complex hydrogeobiochemical processes of streams. The September 2003 Special Issue, "Modeling Hyporheic Zone Processes," of Advances in Water Resources provides several examples of the new directions in which the transient storage concept is being developed.

Topical organization of the Reading List:

The Transient Storage Model
o Simulation of solute transport in a mountain pool-and-riffle stream - a transient storage model. KE Bencala, RA Walters, Water Resources Research, 19(3), 718, 1983.
o One-dimensional transport with inflow and storage (OTIS): a solute transport model for streams and rivers. RL Runkel, USGS WRIR 98-4018, 1998.
[Online at http://co.water.usgs.gov/otis/].
 
Transient Storage - Model Development
Field Data Set
o Results of a solute transport experiment at Uvas Creek, September 1972. RJ Avanzino, GW Zellweger, VC Kennedy, SM Zand, KE Bencala, USGS OFR 84-236, 1984.
 
Application Concepts
o Using OTIS to model solute transport in streams and rivers. RL Runkel, USGS Fact Sheet 138-99, 4 p., 2000.
[Online at http://pubs.water.usgs.gov/fac138-99].
o Quantifying hydrologic interactions between streams and their subsurface hyporheic zones. JW Harvey, BJ Wagner, in Streams and Ground Waters, JB Jones, PJ Mulholland Eds., Academic Press, 3, 2000.
o Experimental design for estimating parameters of rate-limited mass transfer: Analysis of stream tracer studies, BJ Wagner, JW Harvey, Water Resources Research, 33(7), 1731, 1997.
 
Transport Concepts
o Transport of reacting solutes in rivers and streams. RL Runkel, KE Bencala, in Environmental Hydrology, VP Singh Ed., Kluwer Academic Press, 137, 1995.
 
Numerical Method
o An efficient numerical solution of the transient storage equations for solute transport in small streams. RL Runkel, SL Chapra, Water Resources Research, 29, 211, 1993.
 
Transient Storage - Simulation Investigations - Conservative Transport Applications
o Interactions of solutes and streambed sediments - Part 2 A dynamic analysis of coupled hydrologic and chemical processes that determine solute transport. KE Bencala, Water Resources Research, 20(12), 1804, 1984.
o Characterization of transport in an acidic and metal-rich mountain stream based on a lithium tracer injection and simulations of transient storage. KE Bencala, DM McKnight, GW Zellweger, Water Resources Research, 26(5), 989, 1990.
o Tracer-dilution experiments and solute-transport simulations for a mountain stream, Saint Kevin Gulch, Colorado. RE Broshears, KE Bencala, BA Kimball, DM McKnight, USGS WRIR 92-4081, 1993.
o Transient storage in Appalachian and Cascade mountain streams as related to hydraulic characteristics. DJ D'Angelo, JR Webster, SV Gregory, JL Meyer, J North American Benthological Society, 12, 223, 1993.
o Analysis of transient storage subject to unsteady flow: diel flow variation in an Antarctic stream. RL Runkel, DM McKnight, ED Andrews, J North American Benthological Society, 17(2), 143, 1998.
o Transport and concentration controls for chloride, strontium, potassium and lead in Uvas Creek, a small cobble-bed stream in Santa Clara County, California, USA 2. Mathematical model. AP Jackman, RA Walters, VC Kennedy, J Hydrology, 75, 111, 1984.
o Longitudinal dispersion in a forest stream. C LeGrand-Marcq, H Laudelout, J Hydrology, 78, 317, 1985.
 
Transient Storage - Interpretation of Estimated Parameters
o A new metric for determining the importance of transient storage. RL Runkel, J. North American Benthological Society, 21, 529, 2002.
o Evaluating the reliability of the stream tracer approach to characterize stream-subsurface water exchange. JW Harvey, BJ Wagner, KE Bencala, Water Resources Research, 32(8), 2441, 1996.
o Sensitivity analysis of conservative and reactive transient storage models applied to field data from multiple-reach experiments. MN Gooseff, KE Bencala, DT Scott, RL Runkel, DM McKnight,. Advances in Water Resources, 28, 479, 2005.
o Transient storage and hyporheic flow along the Willamette River, Oregon: Field measurements and model estimates, AG Fernald, PJ Wigington, DH Landers, Water Resources Research, 37(6), 1681, 2001.
o Alluvial characteristics, groundwater-surface water exchange, and hydrologic retention in headwater streams. JA Morrice, HM Valett, CN Dahm, ME Campana, Hydrological Processes, 11, 253, 1997.
o The hydraulic characteristics and geochemistry of hyporheic and parafluvial zones in Arctic tundra streams, north slope. KJ Edwardson, WB Bowden, C Dahm, J Morrice, Advances in Water Resources, 26(9), 907, 2003.
o Predicting changes in hydrologic retention in an evolving semi-arid alluvial stream. JW Harvey, MH Conklin, RS Koelsch, Advances in Water Resources, 26(9), 939, 2003.
o Estimation of solute transport and storage parameters in a stream with anthropogenically produced unsteady flow and industrial bromide input. RJ Ryan, AI Packman, C Welty, Water Resources Research, 40, doi:10.1029/2003WR002458, 2004.
o Comparison of transient storage in vegetated and unvegetated reaches of a small agricultural stream in Sweden: seasonal variation and anthropogenic manipulation. M Salehin, AI Packman, A Worman, Advances in Water Resources, 26(9), 951, 2003.
o Determining long time-scale hydrologic flow paths in Antarctic streams. MN Gooseff, DM McKnight, RL Runkel, BH Vaughn, Hydrological Processes, 17(9), 1691, 2003.
o Ground water occurrence and contributions to streamflow in an alpine catchment, Colorado Front Range, DW Clow, L Schrott, R Webb, DH Campbell, A Torizzo, M Dornblaser, Ground Water, 41(1), 937, 2003.
o The influence of aquatic macrophytes on the hydraulic and physico-chemical properties of a New Zealand lowland stream. RJ Wilcock, PD Champion, JW Nagels, GF Croker, Hydrobiologia, 416, 203, 1999.
 
Transient Storage - Parameter Estimation
o Automated calibration of a stream solute transport model: Implications for interpretation of biogeochemical parameters. DT Scott, MN Gooseff, KE Bencala, RL Runkel, Journal of the North American Benthological Society, 22, 492, 2003.
o A stream tracer technique employing ionic tracers and specific conductance data applied to the Maimai catchment, New Zealand. MN Gooseff, BL McGlynn, Hydrological Processes, in press/on-line doi: 10.1002/hyp.5685, 2005.
o A statistical methodology for estimating transport parameters: theory and applications to one-dimensional advective-dispersive systems. BJ Wagner, SM Gorelick, Water Resources Research, 22, 1303, 1986.
o Dynamic identifiability analysis of the transient storage model for solute transport in rivers. T Wagener, LA Camacho, HS Wheater, J. Hydroinformatics, 4, 199, 2002.
o Parameter estimation of the transient storage model by a routing method for river mixing processes. TS Cheong, IW Seo, Water Resources Research, 39(4), doi: 10.1029/2001WR000676, 2003.
 
Transient Storage - Two-Zone Formulation
o Characterizing multiple timescales of stream and storage zone interaction that affect solute fate and transport in streams. J Choi, JW Harvey, MH Conklin, Water Resources Research, 36(6), 1511, 2000.
o Solute transport and storage mechanisms in wetlands of the Everglades, south Florida. JW Harvey, JE Saiers, JT Newlin, Water Resources Research, 41(5), doi: 10.1029/2004WR003507, 2005.
 
Transient Storage - Non-Stream and Non-Conservative Applications
Transient Storage - Wetlands
o Conservative and reactive solute transport in constructed wetlands. SH Keefe, LB Barber, RL Runkel, JN Ryan, DM McKnight, RD Wass, Water Resources Research, 40, doi:10.1029/2003WR002130, 2004.
o Analysis of constructed treatment wetland hydraulics with the transient storage model OTIS. CJ Martinez, WR Wise, Ecological Engineering, 20(3), 211, 2003.
 
Transient Storage - Flume (Periphyton) Parameters
o Contributions of microbial biofilms to ecosystem processes in stream ecosystems. TJ Battin, LA Kaplan, JD Newbold, CME Hansen, Nature, 426, 439, 2003.
o Modeling transient storage and nitrate uptake kinetics in a flume containing a natural periphyton community. BK Kim, AP Jackman, FJ Triska, Water Resources Research, 26, 505, 1990.
o Effect of periphyton biomass on hydraulic characteristics and nutrient cycling in streams. PJ Mulholland, AD Steinman, ER Marzolf, DR Hart, DL DeAngelis, Oecologia, 98, 40, 1994.
 
Transient Storage - Engineered Systems
o Diameter and surcharge effects on solute transport across surcharged manholes, I Guymer, P. Dennis, R O'Brien, C Saiyudthong, J. Hydraulic Engineering. 131, 312, 2005.
 
Transient Storage - Simulation to Parameterize Reactive Transport
o Reach-scale isotope tracer experiment to quantify denitrification and related processes in a nitrate-rich stream, midcontinent United States. JK Bohlke, JW Harvey, MA Voytek, Limnology and Oceanography, 49(3), 821, 2004.
o Particle transport and transient storage along a stream-size gradient in the Hubbard Brook Experimental Forest, MJ Paul, RO Hall Jr., J. North American Benthological Society, 21(2), 195, 2002.
o Stream morphology controls ammonium retention in tropical headwaters. B Gucker, IG Boechat, Ecology, 85(10), 2818, 2004.
o Whole-stream metabolism in two montane streams: contribution of the hyporheic zone. CS Fellows, HM Valett, CN Dahm, Limnology and Oceanography, 46(3), 523, 2001.
o Hydrodynamics is a major determinant of streambed biofilm activity: From the sediment to the reach scale. TJ Battin, Limnology and Oceanography, 45(6), 1308, 2000.
o Reactive iron transport in an acidic mountain stream in Summit County, Colorado: A hydrologic perspective. DM McKnight, KE Bencala, Geochimica et Cosmochimica Acta, 53, 2225, 1989.
o Parent lithology, surface-groundwater exchange and nitrate retention in headwater streams. HM Valett, JA Morrice, CN Dahm, ME Campana, Limnology and Oceanography, 41(2), 333, 1996.
o Evidence that hyporheic zones increase heterotrophic metabolism and phosphorus uptake in forest streams. PJ Mulholland, ER Marzolf, JR Webster, DR Hart, SP Hendricks, Limnology and Oceanography, 42(3), 443, 1997.
o Pre- and post-flood retention efficiency of nitrogen in a Sonoran Desert stream. E Marti, NB Grimm, SG Fischer, J North American Benthological Society, 16(4), 805, 1997.
o Importance of transient storage zones for ammonium and phosphate retention in a sandy-bottom Mediterranean stream. A Butturini, F Sabater, Freshwater Biology, 41, 593, 1999.
o C and N dynamics in the riparian and hyporheic zones of a tropical stream, Luquillo Mountains, Puerto Rico. TJ Chestnut, WH McDowell, J North American Benthological Society, 19(2), 1999, 2000.
 
Transient Storage - Simulation of Reactive Transport
o Transient storage assessments of dye-tracer injections in rivers of the Willamette Basin, Oregon. A Laenen, KE Bencala, J. American Water Resources Association, 37(2), 367, 2001.
o Redox processes controlling manganese fate and transport in a mountain stream, DT Scott, DM McKnight, BM Voelker, DC Hrncir, Environmental Science and Technology, 36(3), 453, 2002.
o Transport and cycling of iron and hydrogen peroxide in a freshwater stream: influence of organic acids. DT Scott, RL Runkel, DM McKnight, BM Voelker, BA Kimball, ER Carraway, Water Resources Research, 39(11), doi: 10.1029/2002WR001768, 2003.
o In-stream sorption of fulvic acid in an acidic stream: A stream-scale transport experiment. DM McKnight, GM Hornberger, KE Bencala, EW Boyer, Water Resources Research, 38(1), doi: 10.1029/2001WR000269, 2002.
o Simulation of solute transport in a mountain pool-and-riffle stream with a kinetic mass transfer model for sorption. KE Bencala, Water Resources Research, 19(3), 732, 1983.
o Performance of sodium as a transport tracer - Experimental and simulation analysis. KE Bencala, in USGS WSP 2270, 83, 1985.
o Coupling of hydrologic transport and chemical reactions in a stream affected by acid mine drainage. BA Kimball, RE Broshears, KE Bencala, DM McKnight, Environmental Science and Technology, 28(12), 2065, 1994.
o Phosphate dynamics in an acidic mountain stream: Interactions involving algal uptake, sorption by iron oxide and photoreduction. CM Tate, RE Broshears, DM McKnight, Limnology and Oceanography, 40(5), 938, 1995.
o Reactive solute transport in streams 1. Development of an equilibrium-based model. RL Runkel, KE Bencala, RE Broshears, SC Chapra, Water Resources Research, 32(2), 409, 1996.
o Reactive solute transport in streams 2. Simulation of a pH modification experiment. RL Runkel, DM McKnight, KE Bencala, SC Chapra, Water Resources Research, 32(2), 419, 1996.
o Reactive solute transport in an acidic stream: Experimental pH increase and simulation of controls on pH, aluminum, and iron. RE Broshears, RL Runkel, BA Kimball, DM McKnight, KE Bencala, Environmental Science and Technology, 30(10), 3016, 1996.
o Reactive solute transport in streams: A surface complexation approach for trace metal sorption. RL Runkel, BA Kimball, DM McKnight, KE Bencala, Water Resources Research, 35(12), 3829, 1999.
o Modeling impact of storage zones on stream dissolved oxygen. SC Chapra, RL Runkel, J Environmental Engineering, 125(5), 415, 1999.
o Transient storage and gas transfer in lowland streams. SC Chapra, RJ Wilcock, J Environmental Engineering, 126(8), 708, 2000.
 
Transient Storage - Simulation of Hyporheic Zone Reactive Transport
o Effect of enhanced manganese oxidation in the hyporheic zone on basin-scale geochemical mass balance. JW Harvey, CC Fuller, Water Resources Research, 34(4), 263, 1998.
o Reach-scale cation exchange controls on major ion chemistry of an Antarctic glacial meltwater stream. MN Gooseff, DM McKnight, RL Runkel, Aquatic Geochemistry, 10(3), 221, 2004.
o Weathering reactions and hyporheic exchange controls on stream water chemistry in a glacial meltwater stream in the McMurdo Dry Valleys. MN Gooseff, DM McKnight, WB Lyons, AE Blum, Water Resources Research, 38(12), 1279, doi:10.1029/2001WR000834, 2002.
o Denitrification and hydrologic transient storage in a glacial meltwater stream, McMurdo Dry Valleys, Antarctica. MN Gooseff, DM McKnight, RL Runkel, and JH Duff, Limnology and Oceanography, 49(5), 1884, 2004.
o Inorganic N and P dynamics of Antarctic glacial meltwater streams as controlled by hyporheic exchange and benthic autotrophic communities. DM McKnight, RL Runkel, CM Tate, JH Duff, DL Moorhead, J. North American Benthological Society, 23(2), 171, 2004.
o A regression approach to estimating reactive solute uptake in advective and transient storage zones of stream ecosystems. SA Thomas, HM Valett, JR Webster, PJ Mulholland, Advances in Water Resources, 26(9), 965, 2003.
o Modeling biotic uptake by periphyton and transient hyporheic storage on nitrate in a natural stream. BKA Kim, AP Jackman, FJ Triska, Water Resources Research, 28(10), 2743, 1992.
 
Environmental Context - Hydrology
o Hyporheic exchange flows. KE Bencala, In Encyclopedia of Hydrological Sciences, MG Anderson, Ed., John Wiley & Sons, In press 2005.
o A perspective on stream-catchment connections. KE Bencala, J. North American Benthological Society, 12(1), 44, 1993.
o Hyporheic zone hydrological processes. KE Bencala, Hydrological Processes, 14, 2797, 2000.
o Modeling surface-subsurface hydrological interactions. Al Packman, KE Bencala, in Streams and Ground Waters, JB Jones, PJ Mulholland, Eds., Academic Press, 45, 2000.
o Ground Water and Surface Water - A Single Resource, TC Winter, JW Harvey, OL Franke, WM Alley, USGS Circular 1139, 1998.
o Abiotic aspects of channels and flood plains in riparian ecology. P Huggenberger, E Hoehn, R Beschta, W Woessner, Freshwater Biology, 40(3 - Rivers in the landscape: riparian and groundwater ecology), 407, 1998.
o River Mixing, JC Rutherford, John Wiley and Sons Ltd, 1994.
 
Related Modeling Forumulations and Applications
o Modeling hyporheic zone processes. RL Runkel, DM McKnight, and H Rajaram, Advances in Water Resources, 26(9), 901, 2003.
o Power-law residence time distribution in the hyporheic zone of a 2nd-order mountain stream. R Haggerty, SM Wondzell, MA Johnson, Geophysical Research Letters, 29(13), 1640, doi:10.1029/2002GL014743, 2002.
o Comparing transient storage modeling and residence time distribution (RTD) analysis in geomorphically varied reaches in the Lookout Creek basin, Oregon, USA . MN Gooseff, SM Wondzell, R Haggerty, J Anderson, Advances in Water Resources, 26(9), 925, 2003.
o A modelling study of hyporheic exchange pattern and the sequence, size, and spacing of stream bedforms in mountain stream networks, Oregon, USA. MN Gooseff, JK Anderson, SM Wondzell, J laNier, R Haggerty, Hydrological Processes, in press/on-line doi: 10.1002/hyp.5790, 2005.
o Surface-subsurface water interactions in an alluviated mountain stream channel, NM Castro, GM Hornberger, Water Resources Research, 27, 1613, 1991.
o Modeling catchment scale mixing in the near-stream zone-Implications for chemical and isotopic hydrograph separation. JG Chanat, GM Hornberger, Geophysical Research Letters, 30, doi:10.1029/2002GL016265, 2003.
o Temporal moments routing in streams and rivers with transient storage. BH Schmid, Advances in Water Resources, 26(9), 1021, 2003.
o Simplification in longitudinal transport modeling: case of instantaneous slug releases. BH Schmid, J. Hydrologic Engineering, 9, 319, 2004.
o On the transient storage equations for longitudinal solute transport in open channels: temporal moments accounting for the effects of first-order decay, BH Schmid, J Hydraulic Research, 33(5), 595, 1995.
o Analytic solution of the transient storage equations accounting for solute decay. BH Schmid, Proceedings of the IAHR, Am Soc Civ Eng, San Francisco, 1997.
o Relationships between hydraulic parameters in a small stream under varying flow and seasonal conditions. DR Hart, PJ Mulholland, ER Marzolf, DL Deangelis, SP Hendricks, Hydrological Processes, 13(10), 1497, 1999.
o Parameter estimation and stochastic interpretation of the transient storage model for solute transport in streams, DR Hart, Water Resources Research, 31, 323, 1995.
o Modelling nutrient-periphyton dynamics in streams with surface-subsurface exchange, CL Dent, JC Henry, Ecological Modelling, 122, 97, 1999.
o On the relationship of transient-storage and aggregated dead zone models to solute transport in streams. MJ Lees, LA Camacho, S Chapra, Water Resources Research, 36(1), 213, 2000.
o Longitudinal dispersion in natural streams, T Beer, PC Young, J Environmental Engineering, 109, 1047, 1983.
o Solute transport and dispersion in channels, PC Young, SG Wallis, in Channel Network Hydrology, K Beven, MJ Kirkby, Eds., John Wiley & Sons Ltd., 129, 1993.
o The active mixing volume: A new concept in modeling environmental systems, PC Young, M Lees, in Statistics for the Environment, V Barnett, KF Turkman Eds., John Wiley & Sons Ltd., 3, 1993.
o Extension of the QUASAR river water quality model to incorporate dead-zone mixing. MJ Lees, L Camacho, P Whitehead, Hydrology and Earth System Sciences, 2, 353, 1998.
o Characterizing in-stream flow refugia. J Lancaster, AG Hildrew, Canadian J Fisheries and Aquatic Sciences, 50, 1663, 1993.
o Hydroecology of river plankton: the role of variability in channel flow. CS Reynolds, Hydrological Processes, 14, 3119, 2000.
o Spatial and temporal changes in phytoplankton abundance in the upper and middle reaches of the River Severn, CS Reynolds, MS Glaister, Arch Hydrobiologia, Supplement, 101(1), 1, 1993.
o A conservative semi-Lagrangian transport model for rivers with transient storage zones. JR Manson, SG Wallis, D Hope, Water Resources Research, 37(12), 3312, 2001.
o Predicting stream transient storage zone characteristics from tracer data. JR Manson, Water Resources Research, 36(2), 629, 2000.
o Comparison of models for transient storage of solutes in small streams. A Wörman, Water Resources Research, 36(2), 455, 2000.
o Application of the transient storage model to analyze advective hyporheic exchange with deep and shallow sediment beds. M Zaramella, AI Packman, A Marion, Water Resources Research, 39, doi:10.1029/2002WR001344, 2003.
o Parameter estimation of the transient storage model for stream-subsurface exchange. A Marion, M Zaramella, AI Packman, J. Environmental Engineering, 129(5), 456, 2003.
o Mountain streams - Modeling hydraulics and substance transport, WK Meier, P Reichert, J. Environmental Engineering, 131(2), 252, 2005.
o Solute transport in open-channel networks in unsteady flow regime. Y Zhang, MM Aral, Environmental Fluid Mechanics, 4, 225, 2004.
o Experimental and numerical validation of the dead-zone model for longitudinal dispersion in rivers. W Czernuszenko, P Rowinski, A Sukhodolov, J Hydraulic Research, 36(2), 269, 1998.
o Incorporating transient storage in conjunctive stream-aquifer modeling. YC Lin, MA Medina Jr., Advances in Water Resources, 26(9), 1001, 2003.
o A methodolgy for solute transport in unsteady, nonuniform streaflow with subsurface interaction . YC Lin, MS Chang, MA Medina Jr., Advances in Water Resources, In press, 2005.
o Unsaturated hyporheic zone flow in stream/aquifer conjunctive systems. GA Fox, DS Durnford, Advances in Water Resources, 26(9), 989, 2003.
 
Hydrometric Observation & Interpretation of Exchange Flows
o The effect of streambed topography on surface-subsurface water exchange in mountain catchments. JW Harvey, KE Bencala, Water Resources Research, 29(1), 89, 1993.
o Geomorphic controls on hyporheic exchange flow in mountain streams. T Kasahara, SM Wondzell, Water Resources Research, 39(1), 1005, doi:10.1029/2002WR001386, 2003.
o Patterns in stream longitudinal profiles and implications for hyporheic exchange flow at the HJ Andrews Experimental Forest, Oregon, USA. JK Anderson, SM Wondzell, MN Gooseff, R Haggerty, Hydrological Processes, in press/on-line doi: 10.1002/hyp.5791, 2005.
o Seasonal and storm dynamics of the hyporheic zone of a 4th-order mountain stream. I: Hydrologic processes, SM Wondzell, FJ Swanson, J North American Benthological Society, 15(1), 3, 1996.
o Factors controlling riffle-scale hyporheic exchange flows and their seasonal changes in a gaining stream: A three-dimensional groundwater flow model. RG Storey, KWF Howard, DD Williams, Water Resources Research, 39, doi:10.1029/2002WR001367, 2003.
o Convective transport within stable river sediments, SA Savant, DD Reible, LJ Thibodeaux, Water Resources Research, 23, 1763, 1987.
o Testing and comparison of four ionic tracers to measure streamflow loss by multiple tracer injection. GW Zellweger, Hydrological Processes, 8, 155, 1994.
o Comparison of tracer-dilution and current-meter discharge measurements in a small gravel-bed stream, Little Lost Man Creek, California. GW Zellweger, RJ Avanzino, KE Bencala, USGS WRIR 89-4150, 1989.
o Use of tracer injections and synoptic sampling to measure metal loading from acid mine drainage, BA Kimball, USGS Fact Sheet 245-96, 1997.
[Online at http://ut.water.usgs.gov/usgsabout/fs245/245.html].
o Quantifying groundwater discharge to a small perennial stream in southern Ontario, Canada, EE Cey, DL Rudolph, GW Parkin, R Aravena, J Hydrology, 210, 21, 1998.
o Seasonal variation in surface-subsurface water exchange and lateral hyporheic area of two stream-aquifer systems. GJ Wroblicky, ME Campana, HM Valett, CN Dahm, Water Resources Research, 34(3), 317, 1998.
o Floods, channel change, and the hyporheic zone. SM Wondzell, FJ Swanson, Water Resources Research, 35(2), 555, 1999.
o Stream and fluvial plain ground water interactions: rescaling hydrogeologic thought. WW Woessner, Ground Water, 38(3), 423, 2000.
o A simple device for measuring differences in hydraulic head between surface water and shallow ground water. RB Wanty, TC Winter, USGS Fact Sheet 077-00, 2000.
o Determination of groundwater discharge into a sand and gravel bottom river: a comparison of chloride dilution and seepage meter techniques. JH Duff, B Toner, AP Jackman, RJ Avanzino, FJ Triska, Verh. Internat. Verein. Limnol., 27, 406, 2000.
o Influence of diurnal variations in stream temperature on streamflow loss and groundwater recharge. J Constantz, CL Thomas, G Zellweger, Water Resources Research, 30(8), 3253, 1994.
o Comparison of heat and bromide ass ground water tracers near streams. J Constantz, MH Cox, GW Su, Ground Water, 41(5), 647, 2003.
o Thermal heterogeneity, stream channel morphology, and salmonid abundance in northeastern Oregon streams. JL Ebersole, WF Liss, CA Frissell, Canadian Journal of Fisheries and Aquatic Sciences, 60, 1266, 2003.
o Stream temperatures in two shaded reaches below cutblocks and logging roads: downstream cooling linked to subsurface hydrology. A Story, RD Moore, JS Macdonald, Canadian Journal of Forest Research, 33(8), 1383, 2003.
o Redd site selection and spawning habitat use by fall chinook salmon: The importance of geomorphic features in large rivers. DR Geist, DD Dauble, Environmental Management, 22(5), 655, 1998.
o Hyporheic discharge of river water into fall chinook salmon (Oncorhynchus tshawytscha) spawning areas in the Hanford Reach, Columbia River, DR Geist, Canadian Journal of Fisheries and Aquatic Sciences, 57(8), 1647, 2000.
o Ground penetrating radar for assessing sediment structures in the hyporheic zone of a prealpine river, MW Naegeli, P Huggenberger, U Uehlinger, J North American Benthological Society, 15(3), 353, 1996.
o Flow-induced uptake of particulate matter in permeable sediments, M Huettel, W Ziebis, S Forster, Limnology and Oceanography, 41(2), 309, 1996.
o Effect of flow-induced exchange in hyporheic zones on longitudinal transport of solutes in streams and rivers. A Worman, AI Packman, H Johansson, K Jonsson, Water Resources Research, 38(1), doi:10.1029/2001WR000769, 2002.
o Hyporheic exchange with gravel beds: Basic hydrodynamic interactions and bedform-induced advective flows. AI Packman, M Salehin, M Zaramella, J. Hydraulic Engineering, 130(7), 647, 2004.
o Hyporheic exchange with heterogeneous streambeds: Laboratory experiments and modeling, M Salehin, AI Packman, M Paradis, Water Resources Research, 40, doi:10.1029/2003WR002567, 2004.
o Relative roles of stream flow and sedimentary conditions in controlling hyporheic exchange. AI Packman, M Salehin, Hydrobiologia, 494, 291, 2003.
o Effect of bed form geometry on the penetration of nonreactive solutes into a streambed. A Marion, M Bellinello, I Guymer, A Packman, Water Resources Research, 38, doi:10.1029/ 2001WR000264, 2002.
o Interplay of stream-subsurface exchange, clay particle deposition, and streambed evolution. AI Packman, JS MacKay, Water Resources Research, 39, doi:10.1029/2002WR001432, 2003.
o Transfer of nonsorbing solutes to a streambed with bed forms: Theory, AH Elliott, NH Brooks, Water Resources Research, 33(1), 123, 1997.
o Transfer of nonsorbing solutes to a streambed with bed forms: Laboratory Experiments, AH Elliott, NH Brooks, Water Resources Research, 33(1), 137, 1997.
o Impact of heterogeneity, bed forms, and stream curvature on subchannel hyporheic exchange. MB Cardenas,JL Wilson, VA Zlotnik, Water Resources Research, 40, doi:10.1029/2004WR003008, 2004.
o Three-dimensional model of modern channel bend deposits. MB Cardenas, VA Zlotnik, Water Resources Research, 39, doi:10.1029/2002WR001383, 2003.
o Effects of porous bed on turbulent stream flow above bed, C Mendoza, D Zhou, J Hydraulic Engineering, 118, 1222, 1992.
 
Transport Characterizations of Exchange Flows
o Evaluation of tracer tests completed in 1999 and 2000 on the upper Santa Clara River, Los Angeles and Ventura Counties, California. MH Cox, GO Mendez, CR Kratzer, EG Reichard, USGS Water-Resources Investigations Report 03-4277, 2003.
[Online at http://water.usgs.gov/pubs/wri/wrir034277/]/.
o Linking hyporheic flow and nitrogen cycling near the Willamette River - a large river in Oregon, U.S.A., SR Hinkle, JH Duff, FJ Triska, A Laenen, EB Gates, KE Bencala, DA Wentz, SR Silva, J. Hydrology, 244, 157, 2001.
o Hydrological influences on hyporheic water quality: implications for salmon egg survival. IA Malcolm, C Soulsby, AF Youngson, DM Hannah, IS McLaren, A Thorne, Hydrological Processes, 18, 1543, 2004.
o Relating nutrient uptake with transient storage in forested mountain streams. RO Hall Jr., ES Bernhardt, GE Likens, Limnology and Oceanography, 47(1), 255, 2002.
o Factors affecting ammonium uptake in streams an inter-biome perspective. JR Webster, PJ Mulholland, JL Tank, HM Valett, WK Dodds, BJ Peterson, WB Bowden, CN Dahm, S Findlay, SV Gregory, NB Grimm, SK Hamilton, SL Johnson, E Martí, WH Mcdowell, JL Meyer, DD Morrall, SA Thomas, WM Wollheim, Freshwater Biology, 48(8), 1329, 2003.
o A mixing model analysis of stream solute dynamics and the contribution of a hyporheic zone to ecosystem function. TJ Battin, LAKaplan, JD Newbold, SP Hendricks, Freshwater Biology, 48(6), 995, 2003.
o The influence of particle size on seston deposition in streams. SA Thomas, JD Newbold, MT Monaghan, GW Minshall, T Georgian, CE Cushing, Limnology and Oceanography, 46(6), 1415, 2001.
o Transport and concentration controls for chloride, strontium, potassium and lead in Uvas Creek, a small cobble-bed stream in Santa Clara County, California, USA 1. Conceptual model. VC Kennedy, AP Jackman, SM Zand, GW Zellweger, RJ Avanzino, J Hydrology, 75, 67, 1984.
o Interactions of solutes and streambed sediments - Part 1 An experimental analysis of cation and anion transport in a mountain stream. KE Bencala, VC Kennedy, GW Zellweger, AP Jackman, RJ Avanzino, Water Resources Research, 20(12), 1797, 1984.
o Rapid flow through the sediments of a headwater stream in the southern Appalachians, NL Munn, JL Meyer, Freshwater Biology, 20, 235, 1988.
o Retention and transport of nutrients in a third-order stream in Northwestern California: Hyporheic processes. FJ Triska, VC Kennedy, RJ Avanzino, GW Zellweger, KE Bencala, Ecology, 70(6), 1877, 1989.
o Biological relationships to convective flow patterns within streambeds, DS White, Hydrobiologia, 196, 149, 1990.
o Hyporheic processes during flooding and drying in a Sonoran Desert stream. I. Hydrologic and chemical dynamics. EH Stanley, AJ Boulton, Arch Hydrobiologia, 134(1), 1, 1995.
o Seasonal biogeochemical patterns in surface water, subsurface hyporheic, and riparian water in a temperate stream, SP Hendricks, DS White, Arch Hydrobiologia, 134(4), 459, 1995.
o Hydrologic and geochemical effects on oxygen uptake in bottom sediments of an effluent-dominated river, PB McMahon, JA Tindal, JA Collins, KJ Lull, JR Nuttle, Water Resources Research, 31, 2561, 1995.
o Vertical hydrologic exchange and ecosystem metabolism in a Sonoran Desert stream. JB Jones, SG Fisher, NB Grimm, Ecology, 76(3), 942, 1995.
o Thermal profiles within river beds, EC Evans, MT Greenwood, GE Petts, Hydrological Processes, 9, 19, 1995.
o Invertebrate drift and longitudinal transport processes in streams, J Lancaster, AG Hildrew, C Gjerlov, Canadian J Fisheries and Aquatic Sciences, 53, 572, 1996.
o Hydrologic influences on groundwater-surface water ecotones: heterogeneity in nutrient composition and retention, HM Valett, CN Dahm, ME Campana, JA Morrice, MA Baker, CS Fellows, J North American Benthological Society, 16(1), 239, 1997.
o Linking the hydrologic and biogeochemical controls of nitrogen transport in near-stream zones of temperate-forested cathments: a review. CP Cirmo, JJ McDonnell, J Hydrology, 199, 88, 1997.
 
Reactive Transport in Surface-Subsurface Water Exchange
o Reactive uptake of trace metals in the hyporheic zone of a mining-contaminated stream, Pinal Creek, Arizona. CC Fuller, JW Harvey, Environmental Science and Technology, 34(7), 1150, 2000.
o Arsenic mobilization in the hyporheic zone of a contaminated stream. SA Nagorski, JN Moore, Water Resources Research, 35(11), 3441, 1999.
o Sorption behavior and long-term retention of reactive solutes in the hyporheic zone of streams. K Jonsson, H Johansson, A Wörman, J. Environmental Engineering, 130, 573, 2004.
o Hyporheic exchange of reactive and conservative solutes in streams-tracer methodology and model interpretation. K Jonsson, H Johansson, A Wörman, Journal of Hydrology, 278(1-4), 153, 2003.
o The effects of partly irreversible solute exchange: comparison between conservative and sorptive transport in streams. KJ Forsman, H Johansson, K Jonsson, Journal of Hydrology, 256(1-2), 15, 2002.
o Retention of conservative and sorptive solutes in streams - simultaneous tracer experiments. H Johansson, K Jonsson, KJ Forsman, A Wörman, The Science of The Total Environment, 266(1-3), 229, 2001.
o Effect of sorption kinetics on the transport of solutes in streams. K Jonsson, A Wörman, The Science of The Total Environment, 266(1-3), 239, 2001.
o Effects of background water composition on stream-subsurface exchange of submicron colloids. J Ren, AI Packman, J. Environmental Engineering, 128(7), 1, 2002.
o Stream-substream exchange of zinc in the presence of silica and kaolinite colloids. J Ren, AI Packman, Environmental Science and Technology, 38(24), 6571, 2004.
o Modeling of simultaneous exchange of colloids and sorbing contaminants between streams and streambeds. J Ren, AI Packman, Environmental Science and Technology, 38(10), 2901, 2004.
o Inorganic nitrogen transformations in the bed of the Shingobee River, Minnesota - Integrating hydrologic and biological processes using sediment perfusion cores. RW Sheibley, JH Duff, AP Jackman, FJ Triska, Limnology and Oceanography, 48, 1129, 2003.
o Numerical modeling of coupled nitrification-denitrification in sediment perfusion cores from the hyporheic zone of the Shingobee River, MN. RW Sheibley, AP Jackman, JH Duff, FJ Triska, Advances in Water Resources, 26(9), 987, 2003.
o Influences of the stream groundwater hydrology on nitrate concentration in unsaturated riparian area bounded by an intermittent Mediterranean stream. A Butturini, S Bernal, C Hellin, E Nin, L Rivero., S Sabater, F Sabater, Water Resources Research, 39, doi:10.1029/2001WR001260, 2003.
o Influence of benthic and interstitial processes on nutrient changes along a regulated reach of a large river (Rhône River, France). G Fauvet, C Claret, P Marmonier, Hydrobiologia, 445, 121, 2001.
o Controlled release experiments to determine the effects of shade and plants on nutrient retention in a lowland stream. RJ Wilcock, MR Scarsbrook, KJ Costley, JW Nagels, Hydrobiologia, 485, 153, 2002.
o Dynamics of abiotic parameters, solute removal and sediment retention in summer-dry headwater streams of western Oregon. M Dieterich, NH Anderson, Hydrobiologia, 379, 1, 1998.
o Hydromorphological control of phosphorus in a large free-flowing gravel bed river: The Gargonne River (France). SB garay, S Sauvage, P Vervier, Regulated Rivers: Research & Management, 17, 46, 2001.
o Hydrologic exchange and N uptake by riparian vegetation in an arid-land stream. JD Schade, JR Welter, E Martí, NB Grimm, J. North American Benthological Society, 24(1), 19, 2005.
o Sediment-water interaction in a small stream: adsorption of 137Cs by bed load sediments, TE Cerling, SJ Morrison, RW Sobcinski, Water Resources Research, 26, 1165, 1990.
o Transport of adsorbing metals from stream water to a stationary sand-bed in a laboratory flume. H Eylers, NH Brooks, JJ Morgan, Marine and Freshwater Research, 46, 209, 1995.
o Metal behavior during surface-groundwater interaction, Silver Bow Creek, Montana. SG Benner, EW Smart, JN Moore, Environmental Science and Technology, 29(7), 1789, 1995.
o Modelling nutrient-periphyton dynamics in streams: the importance of transient storage zones. DL DeAngelis, M Loreau, D Neergaard, PJ Mulholland, ER Marzolf, Ecological Modelling, 80, 149, 1995.
o Diel variation of trace metals in the Upper Clark Fork River, Montana. CM Brick, JN Moore, Environmental Science and Technology, 30(7), 1953, 1996.
o The hyporheic zone as a source of dissolved organic carbon and carbon gases to a temperate forested stream. JE Schindler, DP Krabbenhoft, Biogeochemistry, 43, 157, 1998.
o Nutrient dynamics at the interface between surface waters and groundwaters. CN.Dahm, NB Grimm, P Marmonier, HM Valett, P Vervier, Freshwater Biology, 40(3 - Rivers in the landscape: riparian and groundwater ecology), 427, 1998.
o A mini drivepoint sampler for measureing pore-water solute concentrations in the hyporheic zone of sand-bottom streams. JH Duff, F Murphy, CC Fuller, FJ Triska, JW Harvey, AP Jackman, Limnology and Oceanography, 43(6), 1378, 1998.
o Hydrologic flow paths control dissolved organic carbon fluxes and metabolism in an alpine stream hyporheic zone. TJ Battin, Water Resources Research, 35(10), 3159, 1999.
o Colmation and depth filtration within streambeds: Retention of particles in hyporheic interstices. M Brunke, International Review of Hydrobiology, 84(2), 99, 1999.
o Relationships between metals and hyporheic invertebrate community strucure in a river recovering from metal contamination. SM Nelson, RA Roline, Hydrobiologia, 397, 211, 1999.
o Physical factors influencing fine organic particle transport and deposition in streams. GW Minshall, SA Thomas, JD Newbold, MT Monaghan, CE Cushing, J North American Benthological Society, 19(1), 1, 2000.
o A physicochemical model for colloid exchange between a stream and a sand streambed with bed forms. AI Packman, NH Brooks, JJ Morgan, Water Resources Research, 36(8), 2351, 2000.
o Kaolinite exchange between a stream and streambed: Laboratory experiments and validation of a colloid transport model. AI Packman, NH Brooks, JJ Morgan, Water Resources Research, 36(8), 2363, 2000.
o Hyporheic exchange of solutes and colloids with moving bed forms, AI Packman, NH Brooks, Water Resources Research, 37(10), 2605, 2001.
 
Environmental Context - Ecology
o Surface-subsurface exchange and nutrient spiralling. PJ Mulholland, DL DeAngelis, in Streams and Ground Waters, JB Jones, PJ Mulholland Eds., Academic Press, 149, 2000.
o Surface-subsurface interactions: past, present, and future. EH Stanley, JB Jones, in Streams and Ground Waters, JB Jones, PJ Mulholland Eds., Academic Press, 405, 2000.
o A landscape perspective of surfacesubsurface hydrological exchanges in river corridors. F Malard, K Tockner, M Dole-Olivier, JV Ward, Freshwater Biology, 47(4), 621, 2002.
o The Hyporheic Zone. RT Edwards, in River Ecology and Management: Lessons from the Pacific Coastal Ecoregion. RJ Naiman, RE Bilby Eds., Springer-Verlag, 399, 1998.
o Concepts and methods for assessing solute dynamics in stream ecosystems. Stream Solute Workshop, J North American Benthological Society, 9(2), 95, 1990.
o Stream Ecology, JD Allan, Chapman & Hall, 1995.
o The ecological significance of exchange processes between rivers and groundwater. M Brunke, T Gonser, Freshwater Biology, 37, 1, 1997.
o Modelling within the stream-catchment continuum. KE Bencala, JH Duff, JW Harvey, AP Jackman, FJ Triska, in Modelling Change in Environmental Systems. AJ Jakeman, MB Beck, MJ McAleer Eds., John Wiley & Sons Ltd, 163, 1993.
 

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U.S. Geological Survey
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