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.
Significance of biomass and light availability to phytoplankton productivity in San Francisco Bay
Temporal dynamics and ecological significance of salinity stratification in an estuary (south San-Francisco Bay, USA)
Chemical determination of particulate nitrogen in San Francisco Bay. A comparison of two estimates
Chemical determination of particulate nitrogen in San Francisco Bay. Nitrogen: chlorophyll a ratios in plankton
River discharge controls phytoplankton dynamics in the northern San Francisco Bay estuary
Chemistry and microbiology of a sewage spill in South San Francisco Bay
Does the benthos control phytoplankton biomass in South San Francisco Bay?
Hydrographic properties and primary productivity of San Francisco Bay waters, March 1976-July 1977
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: 93Significance of biomass and light availability to phytoplankton productivity in San Francisco Bay
Primary productivity was measured monthly at 6 sites within San Francisco Bay, USA, throughout 1980. The 6 sites were chosen to represent a range of estuarine environments with respect to salinity, phytoplankton community composition, turbidity, and water depth. Annual net production over the photic zone ranged from 95 to 150 g C m-2, and was highest in regions of lowest turbidity. Daily photic zoAuthorsBrian E. Cole, James E. CloernTemporal dynamics and ecological significance of salinity stratification in an estuary (south San-Francisco Bay, USA)
South San Francisco Bay (USA) has periodic variations in salinity stratification that coïncide with neap-spring tidal variations during the winter "wet" season, but it remains well-mixed during summer and fall. The degree of salinity stratification, and timing of stratification events, can be predicted from a simple empirical function of river discharge and tidal current speed. During periods of pAuthorsJames E. CloernChemical determination of particulate nitrogen in San Francisco Bay. A comparison of two estimates
Particulate nitrogen was measured by both the ultra-violet light-catalyzed peroxide method and the high temperature combustion method. The difference between values obtained with the two methods (combustion minus UV) was found to be linearly correlated with the concentration of total suspended particulate matter (SPM) in the sample. The slope of this correlation was taken to be the concentration oAuthorsS.W. Hager, D.D. HarmonChemical determination of particulate nitrogen in San Francisco Bay. Nitrogen: chlorophyll a ratios in plankton
Particulate nitrogen (PN) and chlorophyll a (Chla) were measured in the northern reach of San Francisco Bay throughout 1980. The PN values were calculated as the differences between unfiltered and filtered (0·4 μm) samples analyzed using the UV-catalyzed peroxide digestion method. The Chla values were measured spectrophotometrically, with corrections made for phaeopigments. The plot of all PNChlaAuthorsS.W. Hager, D.D. Harmon, A.E. AlpineRiver discharge controls phytoplankton dynamics in the northern San Francisco Bay estuary
Phytoplankton dynamics in the upper reach of the northern San Francisco Bay estuary are usually characterized by low biomass dominated by microflagellates or freshwater diatoms in winter, and high biomass dominated by neritic diatoms in summer. During two successive years of very low river discharge (the drought of 1976-77), the summer diatom bloom was absent. This is consistent with the hypothesiAuthorsJ. E. Cloern, A.E. Alpine, B.E. Cole, R.L.J. Wong, J.F. Arthur, M.D. BallChemistry and microbiology of a sewage spill in South San Francisco Bay
During three weeks of September 1979, the breakdown of a waste treatment plant resulted in the discharge of a large volume (1.5×107m3) of primary-treated sewage into a tributary of South San Francisco Bay, California. Chemical and microbial changes occurred within the tributary as decomposition and nitrification depleted dissolved oxygen. Associated with anoxia were relatively high concentrationsAuthorsJ. E. Cloern, R.S. OremlandDoes the benthos control phytoplankton biomass in South San Francisco Bay?
South San Francisco Bay, USA, is a shallow coastal embayment that receives large inputs of nutrients (N. P, Si) and small local inputs of freshwater. Phytoplankton dynamics are typically characterized by a spring bloom when surface chlorophyll a increases from < 5 to > 40 mg m-3. The bloom persists for 2 to 4 wk, and then dissipates. Phytoplankton biomass remains low (chlorophyll a < 5 mg m-3) froAuthorsJames E. CloernHydrographic properties and primary productivity of San Francisco Bay waters, March 1976-July 1977
Data are presented on the quantitative relations between water chemistry and phytoplankton productivity in San Francisco Bay between March 1976 and July 1977. Spatial distributions are listed for: salinity, temperature, transmission, chlorophyll-a, fluorescence, dissolved oxygen, orthophosphate, nitrate + nitrite, nitrite, ammonia, particulate organic carbon, alkalinity, pH, pCO2, suspended sedimeAuthorsBrian E. Cole, Raynol E. Herndon - 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: