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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

Bearman, J., Friedrichs, C., Jaffe, B.E., and Foxgrover, 2010, Spatial trends in tidal flat shape and associated environmental parameters in South San Francisco Bay, Journal of Coastal Research, v. 26, no. 2, p. 342-349.

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.

Bouse, R.M., Fuller, C.F., Luoma, S.N., Hornberger, M.I., Jaffe, B.E., and Smith, R. E., 2010, Mercury-Contaminated Hydraulic Mining Debris in San Francisco Bay, San Francisco Estuary and Watershed Science, v. 8, no. 1, 28 p., http://escholarship.org/uc/item/15j0b0z4.

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.

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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.

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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.

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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.

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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.

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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.

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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.

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