Water Quality of San Francisco Bay Research and Monitoring Project Active
Since 1969, the U.S. Geological Survey has maintained a research project in the San Francisco Bay-Delta system to measure and understand how estuarine systems and tidal river deltas function and change in response to hydro-climatic variability and human activities.
Project Overview
Estuaries are the interface of rivers, ocean, atmosphere, and dense human settlement. As such, their variability is driven by a large array of natural and anthropogenic forces. This website describes the long-term research and observation project in the San Francisco Bay-Delta that serves to measure and understand changes in water quality due to these forces.
For the past five decades, the USGS has conducted ship-based measurements of water quality along a 145-kilometer-deep water transect that spans the length of the entire system from ocean to inland delta. We sample the full salinity gradient on monthly cruises aboard the R/V Peterson and historically on the R/V Polaris. Read more about where and when we collect measurements.
We measure the basic elements of water quality that define the sustainability of the Bay as habitat for fish and organisms of the lower trophic levels. Using both oceanographic sensors and discrete water collection, we measure salinity, temperature, light extinction coefficient, chlorophyll-a, dissolved oxygen, suspended particulate matter, nitrate, nitrite, ammonium, silicate, and phosphate. Take a closer look at what we measure and how our measurements are made.
Data availability
Access the Water Quality of San Francisco Bay Data Query to download measurements from 1969 to our most recent cruise.
These publicly available data are used to measure, model, and understand how estuaries function as transitional ecosystems between land and sea where seawater and freshwater meet. We provide examples of the diversity of applications of these data used in many different disciplines that range from tidal circulation and transport processes and sediment-water nutrient exchange, to phytoplankton productivity and responses to climate variability.
Data visualizations for each cruise will be added to this site in the near future.
Science Communications
- Patterns and Processes of Change Where Rivers Meet Oceans: presentation by James Cloern for Moss Landing Marine Laboratories, 2021.
- Chasing the Spring Phytoplankton Bloom: presentation by Tara Schraga at the Exploratorium museum, 2021.
- USGS R/V Polaris Retires: We reflect on what she taught us: poster, 2016.
- How is San Francisco Bay Doing?: presentation by James Cloern for the USGS Public Lecture Series, 2011.
- Four Decades of Water Quality Research in San Francisco Bay: poster, 2009.
- Inside the Golden Gate: Part 1 and Part 2: NOVA television special, filmed aboard the R/V Polaris in 1976
Our Science in the News
- Feel Like the SF Bay Used to Be Bluer? You're Not Imagining It: KQED Podcast and Article, 2019.
- Public radio KALW show, 2016.
- Bay Belle Retires; Catamaran Carries On. Estuary News, 2016.
- Monitoring San Francisco Bay water critical for future. ABC13 News, 2014.
- San Francisco Bay waters are becoming clearer, but that may mean threats from algal growth. San Jose Mercury News, 2013.
- Climate change may transform California's Bay Area. Scientific American, 2011.
Agencies Supporting the Program of Water-Quality Data Collection and Dissemination
- U.S. Geological Survey Water Resources Division (2017 to present), National Research Program (until 2017)
- U.S. Geological Survey San Francisco Bay Priority Landscapes Program
- U.S. Geological Survey California Water Science Center
- San Francisco Estuary Institute: The Regional Monitoring Program
- San Francisco Estuary Institute: San Francisco Bay Nutrient Management Strategy
This work complements the Interagency Ecological Program for the San Francisco Bay/Delta Ecosystem.
Below are other science pages associated with the Water Quality of San Francisco Bay project.
Directly measured parameter data (depth, chlorophyll-a, dissolved oxygen, suspended particulate matter, extinction coefficient, salinity, temperature, nutrients) are available from the locations below:
Below are multimedia items associated with the Water Quality of San Francisco Bay project.
Below are publications associated with the Water Quality of San Francisco Bay project.
Comparative biogeochemistry-ecosystem-human interactions on dynamic continental margins
Phytoplankton primary production in the world's estuarine-coastal ecosystems
Resource selection and space use by sea ducks during the non-breeding season: Implications for habitat conservation planning in urbanized estuaries
Factors controlling floc settling velocity along a longitudinal estuarine transect
A step decrease in sediment concentration in a highly modified tidal river delta following the 1983 El Niño floods
Distribution of biologic, anthropogenic, and volcanic constituents as a proxy for sediment transport in the San Francisco Bay Coastal System
A sediment budget for the southern reach in San Francisco Bay, CA: Implications for habitat restoration
Integration of bed characteristics, geochemical tracers, current measurements, and numerical modeling for assessing the provenance of beach sand in the San Francisco Bay Coastal System
Over 150 million m3 of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent
Influence of estuarine processes on spatiotemporal variation in bioavailable selenium
Drivers of change in estuarine-coastal ecosystems: Discoveries from four decades of study in San Francisco Bay
Changing restoration rules: exotic bivalves interact with residence time and depth to control phytoplankton productivity
Sudden clearing of estuarine waters upon crossing the threshold from transport to supply regulation of sediment transport as an erodible sediment pool is depleted: San Francisco Bay, 1999
Directly measured parameter data (depth, chlorophyll-a, dissolved oxygen, suspended particulate matter, extinction coefficient, salinity, temperature, nutrients) are available from the locations below:
- Overview
Since 1969, the U.S. Geological Survey has maintained a research project in the San Francisco Bay-Delta system to measure and understand how estuarine systems and tidal river deltas function and change in response to hydro-climatic variability and human activities.
Project Overview
Estuaries are the interface of rivers, ocean, atmosphere, and dense human settlement. As such, their variability is driven by a large array of natural and anthropogenic forces. This website describes the long-term research and observation project in the San Francisco Bay-Delta that serves to measure and understand changes in water quality due to these forces.
For the past five decades, the USGS has conducted ship-based measurements of water quality along a 145-kilometer-deep water transect that spans the length of the entire system from ocean to inland delta. We sample the full salinity gradient on monthly cruises aboard the R/V Peterson and historically on the R/V Polaris. Read more about where and when we collect measurements.
We measure the basic elements of water quality that define the sustainability of the Bay as habitat for fish and organisms of the lower trophic levels. Using both oceanographic sensors and discrete water collection, we measure salinity, temperature, light extinction coefficient, chlorophyll-a, dissolved oxygen, suspended particulate matter, nitrate, nitrite, ammonium, silicate, and phosphate. Take a closer look at what we measure and how our measurements are made.
Data availability
Access the Water Quality of San Francisco Bay Data Query to download measurements from 1969 to our most recent cruise.
These publicly available data are used to measure, model, and understand how estuaries function as transitional ecosystems between land and sea where seawater and freshwater meet. We provide examples of the diversity of applications of these data used in many different disciplines that range from tidal circulation and transport processes and sediment-water nutrient exchange, to phytoplankton productivity and responses to climate variability.
Data visualizations for each cruise will be added to this site in the near future.
Science Communications
- Patterns and Processes of Change Where Rivers Meet Oceans: presentation by James Cloern for Moss Landing Marine Laboratories, 2021.
- Chasing the Spring Phytoplankton Bloom: presentation by Tara Schraga at the Exploratorium museum, 2021.
- USGS R/V Polaris Retires: We reflect on what she taught us: poster, 2016.
- How is San Francisco Bay Doing?: presentation by James Cloern for the USGS Public Lecture Series, 2011.
- Four Decades of Water Quality Research in San Francisco Bay: poster, 2009.
- Inside the Golden Gate: Part 1 and Part 2: NOVA television special, filmed aboard the R/V Polaris in 1976
Our Science in the News
- Feel Like the SF Bay Used to Be Bluer? You're Not Imagining It: KQED Podcast and Article, 2019.
- Public radio KALW show, 2016.
- Bay Belle Retires; Catamaran Carries On. Estuary News, 2016.
- Monitoring San Francisco Bay water critical for future. ABC13 News, 2014.
- San Francisco Bay waters are becoming clearer, but that may mean threats from algal growth. San Jose Mercury News, 2013.
- Climate change may transform California's Bay Area. Scientific American, 2011.
Agencies Supporting the Program of Water-Quality Data Collection and Dissemination
- U.S. Geological Survey Water Resources Division (2017 to present), National Research Program (until 2017)
- U.S. Geological Survey San Francisco Bay Priority Landscapes Program
- U.S. Geological Survey California Water Science Center
- San Francisco Estuary Institute: The Regional Monitoring Program
- San Francisco Estuary Institute: San Francisco Bay Nutrient Management Strategy
This work complements the Interagency Ecological Program for the San Francisco Bay/Delta Ecosystem.
- Science
Below are other science pages associated with the Water Quality of San Francisco Bay project.
- Data
Directly measured parameter data (depth, chlorophyll-a, dissolved oxygen, suspended particulate matter, extinction coefficient, salinity, temperature, nutrients) are available from the locations below:
- Multimedia
Below are multimedia items associated with the Water Quality of San Francisco Bay project.
- Publications
Below are publications associated with the Water Quality of San Francisco Bay project.
Filter Total Items: 93Comparative biogeochemistry-ecosystem-human interactions on dynamic continental margins
The ocean’s continental margins face strong and rapid change, forced by a combination of direct human activity, anthropogenic CO2-induced climate change, and natural variability. Stimulated by discussions in Goa, India at the IMBER IMBIZO III, we (1) provide an overview of the drivers of biogeochemical variation and change on margins, (2) compare temporal trends in hydrographic and biogeochemicalAuthorsLisa A. Levin, Kon-Kee Liu, Kay-Christian Emeis, Denise L. Breitburg, James Cloern, Curtis Deutsch, Michele Giani, Anne Goffart, Eileen E. Hofmann, Zouhair Lachkar, Karin Limburg, Su-Mei Liu, Enrique Montes, Wajih Naqvi, Olivier Ragueneau, Christophe Rabouille, Santosh Kumar Sarkar, Dennis P. Swaney, Paul Wassman, Karen F. WishnerPhytoplankton primary production in the world's estuarine-coastal ecosystems
Estuaries are biogeochemical hot spots because they receive large inputs of nutrients and organic carbon from land and oceans to support high rates of metabolism and primary production. We synthesize published rates of annual phytoplankton primary production (APPP) in marine ecosystems influenced by connectivity to land – estuaries, bays, lagoons, fjords and inland seas. Review of the scientific lAuthorsJames E. Cloern, S.Q. Foster, A.E. KlecknerResource selection and space use by sea ducks during the non-breeding season: Implications for habitat conservation planning in urbanized estuaries
Wide-ranging marine birds rely on multiple habitats for wintering, breeding, and migrating, and their conservation may be dependent on protecting networks of key areas. Urbanized estuaries are critical wintering and stopover areas for many declining sea ducks in North America; however, conservation measures within estuaries are difficult to establish given lack of knowledge about habitat use by thAuthorsSusan E. W. De La Cruz, John M. Eadie, A. Keith Miles, Julie Yee, Kyle A. Spragens, Eric C. Palm, John Y. TakekawaFactors controlling floc settling velocity along a longitudinal estuarine transect
A 147 km longitudinal transect of flocculated cohesive sediment properties in San Francisco Bay (SFB) was conducted on June 17th, 2008. Our aim was to determine the factors that control floc settling velocity along the longitudinal axis of the estuary. The INSSEV-LF video system was used to measure floc diameters and settling velocities at 30 stations at a distance of 0.7 m above the estuary bed.AuthorsA.J. Manning, David H. SchoellhamerA step decrease in sediment concentration in a highly modified tidal river delta following the 1983 El Niño floods
Anthropogenic activities in watersheds can have profound effects on sediment transport through river systems to estuaries. Disturbance in a watershed combined with alterations to the hydro-climatologic regime may result in changes to the sediment flux, and exacerbate the impacts of extreme events (such as large-magnitude floods) on sediment transport. In the San Francisco Estuary, suspended sedimeAuthorsErin L. Hestir, David H. Schoellhamer, Tara Morgan-King, Susan L. UstinDistribution of biologic, anthropogenic, and volcanic constituents as a proxy for sediment transport in the San Francisco Bay Coastal System
Although conventional sediment parameters (mean grain size, sorting, and skewness) and provenance have typically been used to infer sediment transport pathways, most freshwater, brackish, and marine environments are also characterized by abundant sediment constituents of biological, and possibly anthropogenic and volcanic, origin that can provide additional insight into local sedimentary processesAuthorsMary McGann, Li H. Erikson, Elmira Wan, Charles L. Powell, Rosalie F. MaddocksA sediment budget for the southern reach in San Francisco Bay, CA: Implications for habitat restoration
The South Bay Salt Pond Restoration Project is overseeing the restoration of about 6000 ha of former commercial salt-evaporation ponds to tidal marsh and managed wetlands in the southern reach of San Francisco Bay (SFB). As a result of regional groundwater overdrafts prior to the 1970s, parts of the project area have subsided below sea-level and will require between 29 and 45 million m3 of sedimenAuthorsGregory Shellenbarger, Scott A. Wright, David H. SchoellhamerIntegration of bed characteristics, geochemical tracers, current measurements, and numerical modeling for assessing the provenance of beach sand in the San Francisco Bay Coastal System
Over 150 million m3 of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent
AuthorsPatrick L. Barnard, Amy C. Foxgrover, Edwin P.L. Elias, Li H. Erikson, James R. Hein, Mary McGann, Kira Mizell, Robert J. Rosenbauer, Peter W. Swarzenski, Renee K. Takesue, Florence L. Wong, Don WoodrowInfluence of estuarine processes on spatiotemporal variation in bioavailable selenium
Dynamic processes (physical, chemical and biological) challenge our ability to quantify and manage the ecological risk of chemical contaminants in estuarine environments. Selenium (Se) bioavailability (defined by bioaccumulation), stable isotopes and molar carbon-tonitrogen ratios in the benthic clam Potamocorbula amurensis, an important food source for predators, were determined monthly for 17 yrAuthorsA. Robin Stewart, Samuel N. Luoma, Kent A. Elrick, James L. Carter, Mick van der WegenDrivers of change in estuarine-coastal ecosystems: Discoveries from four decades of study in San Francisco Bay
Poised at the interface of rivers, ocean, atmosphere and dense human settlement, estuaries are driven by a large array of natural and anthropogenic forces. San Francisco Bay exemplifies the fast-paced change occurring in many of the world's estuaries, bays and inland seas in response to these diverse forces. We use observations from this particularly well-studied estuary to illustrate responses toAuthorsJ. E. Cloern, A.D. JassbyChanging restoration rules: exotic bivalves interact with residence time and depth to control phytoplankton productivity
Non-native species are a prevalent ecosystem stressor that can interact with other stressors to confound resource management and restoration. We examine how interactions between physical habitat attributes and a particular category of non-native species (invasive bivalves) influence primary production in aquatic ecosystems. Using mathematical models, we show how intuitive relationships between phyAuthorsLisa V. Lucas, Janet K. ThompsonSudden clearing of estuarine waters upon crossing the threshold from transport to supply regulation of sediment transport as an erodible sediment pool is depleted: San Francisco Bay, 1999
The quantity of suspended sediment in an estuary is regulated either by transport, where energy or time needed to suspend sediment is limiting, or by supply, where the quantity of erodible sediment is limiting. This paper presents a hypothesis that suspended-sediment concentration (SSC) in estuaries can suddenly decrease when the threshold from transport to supply regulation is crossed as an erodiAuthorsD. H. Schoellhamer - Web Tools
Directly measured parameter data (depth, chlorophyll-a, dissolved oxygen, suspended particulate matter, extinction coefficient, salinity, temperature, nutrients) are available from the locations below: