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

• Understanding the occurrence and transport of current-use pesticides in the San Francisco Estuary Watershed: Kuivila, K.M., and Hladik, M.L., San Francisco Estuary and Watershed Science (IN PRESS).
• Influence of plankton mercury dynamics and trophic pathways on mercury concentrations of top predator fish of a mining-impacted reservoir: Stewart, A.R., Saiki, M.K., Kuwabara, J.S., Alpers, C.N., Marvin DiPasquale, M., and Krabbenhoft, D.P., Canadian Journal of Fisheries and Aquatic Sciences, v. 65 (IN PRESS).
• 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., Journal of Marine Systems, doi:10.1016/j.jmarsys.2008.07.011 (Corrected Proof) (IN PRESS).
• Corbula amurensis: Thompson, J.K., in Invasive Species Compendium, Wallingford, Oxfordshire, United Kingdom, CABI (IN PRESS).
• 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., Journal of Marine Systems, doi:10.1016/j.jmarsys.2007.12.006 (Corrected proof) (IN PRESS).

Newly Published

• Understanding the occurrence and transport of current-use pesticides in the San Francisco Estuary watershed: Kuivila, K.M., and Hladik, M.L., 2008, San Francisco Estuary and Watershed Science, v. 6, no. 3, Article 2.
• Complex seasonal patterns of primary producers at the land–sea interface: Cloern, J.E., and Jassby, A.D., 2008, Ecology Letters, doi:10.1111/j.1461-0248.2008.01244.x (Advanced Web release).
• A note on the effect of wind waves on vertical mixing in Franks Tract, Sacramento-San Joaquin Delta, California: Jones, N.L., Thompson, J.K., and Monismith, S.G., 2008, San Francisco Estuary and Watershed Science, v. 6, no. 2, p. article 4.
• Primary production and carrying capacity of former salt ponds after reconnection to San Francisco Bay: Thébault, J., Schraga, T.S., Cloern, J.E., and Dunleavy, E.G., 2008, Wetlands, v. 28, no. 3, p. 841-851, doi:10.1672/07-190.1.

Additional USGS Information about San Francisco Bay

• Access USGS San Francisco Bay and Delta

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