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.
Use of the euryhaline bivalve Potamocorbula amurensis as a biosentinel species to assess trace metal contamination in San Francisco Bay
Year-to-year fluctuation of the spring phytoplankton bloom in south San Francisco Bay: An example of ecological variability at the land-sea interface
Notes on a Mesodinium rubrum red tide in San Francisco Bay (California, USA)
Organic carbon sources and sinks in San Francisco Bay: variability induced by river flow
Coupled effects of vertical mixing and benthic grazing on phytoplankton populations in shallow, turbid estuaries
Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary
Annual variations in river flow and primary production in the south San Francisco Bay estuary (USA)
Tidal stirring and phytoplankton bloom dynamics in an estuary
Episodic changes in lateral transport and phytoplankton distribution in South San Francisco Bay
Trace metal associations in the water column of South San Francisco Bay, California
Spatial and temporal variability in South San Francisco Bay (USA). I. Horizontal distributions of salinity, suspended sediments, and phytoplankton biomass and productivity
Spatial and temporal variability in South San Francisco Bay (USA). II. Temporal changes in salinity, suspended sediments, and phytoplankton biomass and productivity over tidal time scales
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: 93Use of the euryhaline bivalve Potamocorbula amurensis as a biosentinel species to assess trace metal contamination in San Francisco Bay
Potamocorbula amurensis was assessed as a biosentinel species in San Francisco Bay, California, USA. Uptake of metal in both the laboratory and field showed that P. amurensis was sufficiently responsive to Ag, Cd, Cr, Ni and V to detect environmental differences in exposure. It was less suitable as an indicator of Cu and Zn contamination. Concentration factors for P. amurensis were: Ag, 386000; CdAuthorsC. L. Brown, S. N. LuomaYear-to-year fluctuation of the spring phytoplankton bloom in south San Francisco Bay: An example of ecological variability at the land-sea interface
Estuaries are transitional ecosystems at the interface of the terrestrial and marine realms. Their unique physiographic position gives rise to large spatial variability, and to dynamic temporal variability resulting, in part, from a variety of forces and fluxes at the oceanic and terrestrial boundaries. River flow, in particular, is an important mechanism for delivering watershed-derived materialsAuthorsJames E. Cloern, Alan D. JassbyNotes on a Mesodinium rubrum red tide in San Francisco Bay (California, USA)
Discrete red patches of water were observed in South San Francisco Bay (USA) on 30 April 1993, and examination of live samples showed that this red tide was caused by surface accumulations of the pigmented ciliate Mesodinium rubrum . Vertical profiles showed strong salinity and temperature stratification in the upper 5 m, peak chlorophyll fluorescence in the upper meter, and differences in the smaAuthorsJames E. Cloern, Brian E. Cole, Stephen W. HagerOrganic carbon sources and sinks in San Francisco Bay: variability induced by river flow
Sources and sinks of organic carbon for San Francisco Bay (California, USA) were estimated for 1980. Sources for the southern reach were dominated by phytoplankton and benthic microalgal production. River loading of organic matter was an additional important factor in the northern reach. Tidal marsh export and point sources played a secondary role. Autochthonous production in San Francisco Bay apAuthorsAlan D. Jassby, T.M. Powell, James E. CloernCoupled effects of vertical mixing and benthic grazing on phytoplankton populations in shallow, turbid estuaries
Coastal ocean waters tend to have very different patterns of phytoplankton biomass variability from the open ocean, and the connections between physical variability and phytoplankton bloom dynamics are less well established for these shallow systems. Predictions of biological responses to physical variability in these environments is inherently difficult because the recurrent seasonal patterns ofAuthorsJeffrey R. Koseff, Jacqueline K. Holen, Stephen G. Monismith, James E. CloernTrophic interactions and direct physical effects control phytoplankton biomass and production in an estuary
San Francisco Bay has recently been invaded by the suspension-feeding clam Potamocorbula amurensis. Previous work has shown that phytoplankton biomass in the upper estuary is low (2-3 mg Chl a m-3) during seasonal periods of high river flow and short residence time and it is usually high (peak >30 mg Chl a m-3) during the summer-autumn seasons of low river flow and long residence time. However sinAuthorsA.E. Alpine, J. E. CloernAnnual variations in river flow and primary production in the south San Francisco Bay estuary (USA)
No abstract available.AuthorsJames E. CloernTidal stirring and phytoplankton bloom dynamics in an estuary
In South San Francisco Bay, estuarine phytoplankton biomass fluctuates at the time scale of days to weeks; much of this variability is associated with fluctuations in tidal energy. During the spring seasons of every year from 1980-1990, episodic blooms occurred in which phytoplankton biomass rose from a baseline of 2-4mg chlorophyll a m-3, peaked at 20-40 chlorophyll a m-3, then returned to baseliAuthorsJ. E. CloernEpisodic changes in lateral transport and phytoplankton distribution in South San Francisco Bay
Increased lateral flows were directed to the west and may explain the large fluctuations in phytoplankton biomass observed over the broad eastern shoal during spring. -from AuthorsAuthorsL.M. Huzzey, J. E. Cloern, T.M. PowellTrace metal associations in the water column of South San Francisco Bay, California
Spatial distributions of copper (Cu), zinc (Zn) and cadmium (Cd) were followed along a longitudinal gradient of dissolved organic carbon (DOC) in South San Francisco Bay (herein referred to as the South Bay). Dissolved Cu, Zn and Cd concentrations ranged from 24 to 66 nM, from 20 to 107 nM and from 1·2 to 4·7 nM, respectively, in samples collected on five dates beginning with the spring phytoplankAuthorsJ.S. Kuwabara, Cecily C.Y. Chang, J. E. Cloern, T. L. Fries, J.A. Davis, S. N. LuomaSpatial and temporal variability in South San Francisco Bay (USA). I. Horizontal distributions of salinity, suspended sediments, and phytoplankton biomass and productivity
The horizontal pattern of mesoscale (1–4 km) variability in salinity was a poor predictor of mesoscale patterns in chlorophyll a, suspended particulate matter, and daily primary productivity in the South San Francisco Bay estuary during spring 1987. The tidally-averaged salinity distribution varied over weekly time scales, reflecting inputs of freshwater as well as transport processes. Spatial disAuthorsT.M. Powell, J. E. Cloern, L.M. HuzzeySpatial and temporal variability in South San Francisco Bay (USA). II. Temporal changes in salinity, suspended sediments, and phytoplankton biomass and productivity over tidal time scales
Short-term variability of a conservative quantity (salinity) and two nonconservative quantities (chlorophyll a, suspended particulate matter) was measured across a sampling grid in the South San Francisco Bay estuary. Surface measurements were made every 2 h at each of 29 (or 38) sites, on four different dates representing a range of tidal current regimes over the neap-spring cycle. From the distrAuthorsJ. E. Cloern, T.M. Powell, L.M. Huzzey - 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: