San Francisco Bay Estuary Priority Ecosystem Study

Diverse organic and inorganic contaminants that vary widely in their environmental behavior, sources, and toxicity enter the San Francisco Bay estuary. Toxic substances enter the estuary in agricultural and urban runoff and in discharges from municipal wastewater facilities and industries. The study focuses on the movement, fate, and effect of contaminants from a variety of agricultural, industrial, and urban sources, such as pesticides and toxic trace elements, and on the effects of the highly varying hydrologic conditions in river--estuarine environments. Scientists are developing an approach to characterize the distribution of contamination and the resulting ecological effects that will be applied in similar environments elsewhere.

Project Headlines

• Climate-Driven Ocean Changes Affect Estuaries: Pacific Ocean Cooling Triggers Phytoplankton Blooms in San Francisco Bay
• Microscopic Phytoplankton Can Cause Big Problems for Estuaries
• Biodynamic Model is Unraveling the Complexities of Metal Bioaccumulation from Contaminated Sediments
• A Tool for Predicting the Effect of Invasive Species on Aquatic Food Webs
• Dr. Samuel N. Luoma Receives 2004 Presidential Rank Award
• New Method for Assessing Bed Sediment Contamination
• USGS Scientist Receives Fulbright Distinguished Scholar Award
• Silver can Affect Fish Reproduction in San Francisco Bay

More Information

• San Francisco Bay Estuary Toxics Site Home Page -- The San Francisco Bay research team maintains it's own home page that contains more up-to-date information.
• Ecology and Contaminants Project
• Geochemistry of Riverine and Estuarine Waters
• Hydrodynamics and Mathematical Modeling of Circulation and Transport Phenomena in Tidal Estuaries
• Solute Transport Involving Biological Processes in Surface Waters
• Water Quality of San Francisco Bay
• Project Bibliography
• Project Photo Gallery
• For additional information about the San Francisco Bay Toxics Site please send e-mail to Kathryn Kuivila at or James Kuwabara at

Project Remediation/Restoration Related Activities

• Nickel Cycling in the South San Francisco Bay
• Evaluation of Selenium Remediation Plans
• Yolo Bypass Studies
• Mercury Transport in the Carson River Basin
• Lake Coeur d'Alene Remediation Assessment

New Publications

Upcoming Publications

• Hydrodynamic control of phytoplankton loss to the benthos in an estuarine environment: Jones, N.L., Thompson, J.K., Arrigo, K.R., and Monismith, S.G., Limnology and Oceanography (IN PRESS).
• Implications of estuarine transport for water quality: Lucas, L.V., in Valle-Levinson, A., ed., Contemporary Issues in Estuarine Physics, New York, Cambridge University Press (IN PRESS).
• Corbula amurensis: Thompson, J.K., in Invasive Species Compendium, Wallingford, Oxfordshire, United Kingdom, CABI (IN PRESS).

Newly Published

• Mercury cycling in stream ecosystems--3. Trophic dynamics and methylmercury bioaccumulation: Chasar, L.C., Scudder, B.C., Stewart, A.R., Bell, A.H., and Aiken, G.R., 2009, Environmental Science and Technology, doi:10.1021/es8027567 (Advanced Web release).
• Benthic nutrient sources to hypereutrophic Upper Klamath Lake, Oregon: Kuwabara, J.S., Topping, B.R., Lynch, D.D., Carter, J.L., and Essaid, H.I., 2009, Environmental Toxicology and Chemistry, v. 28, no. 3, p. 516-524, doi:10.1897/08-207.1.
• Why are diverse relationships observed between phytoplankton biomass and transport time?: Lucas, L.V., Thompson, J.K., and Brown, L.R., 2009, Limnology and Oceanography, v. 54, no. 1, p. 381-390.
• Shallow water processes govern system-wide phytoplankton bloom dynamics--A modeling study: Lucas, L.V., Koseff, J.R., Monismith, S.G., and Thompson, J.K., 2008, Journal of Marine Systems, v. 75, no. 1-2, p. 70-86 doi:10.1016/j.jmarsys.2008.07.011.
• Shallow water processes govern system-wide phytoplankton bloom dynamics--A field study: Thompson, J.K., Koseff, J.R., Monismith, S.G., and Lucas, L.V., 2008, Journal of Marine Systems, v. 74, no. 1-2, p. 153-166, doi:10.1016/j.jmarsys.2007.12.006.
• Environmental factors affecting mercury in Camp Far West Reservoir, 2001-03: Alpers, C.N., Stewart, A.R., Saiki, M.K., Marvin-DiPasquale, M., Topping, B.R., Rider, K.M., Gallanthine, S.K., Kester, C.A., Rye, R.O., Antweiler, R.C., and DeWild, J.F., 2008, U.S. Geological Survey Scientific Investigations Report 2006-5008, 358 p.

Additional USGS Information about San Francisco Bay

• Access USGS San Francisco Bay and Delta

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