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

• 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 (IN PRESS).

Newly Published

• Oceans--On phytoplankton trends: Smetacek, V., and Cloern, J.E., 2008, Science, v. 319, no. 5868, p. 1346-1348, doi:10.1126/science.1151330.
• Using biodynamic models to reconcile differences between laboratory toxicity tests and field biomonitoring with aquatic insects: Buchwalter, D.B., Cain, D.J., Clements, W.H., and Luoma, S.N., 2008, Environmental Science and Technology, doi:10.1021/es703130e (Advanced Web release).
• A biodynamic understanding of dietborne metal uptake by a freshwater invertebrate: Croteau, M.-N., and Luoma, S.N., 2008, Environmental Science and Technology, doi:10.1021/es7022913 (Advanced web release).

Additional USGS Information about San Francisco Bay

• Access USGS San Francisco Bay and Delta

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