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.
Phytoplankton community ecology: Principles applied in San Francisco Bay
Climate anomalies generate an exceptional dinoflagellate bloom in San Francisco Bay
Detritus fuels ecosystem metabolism but not metazoan food webs in San Francisco estuary's freshwater delta
One estuary, one invasion, two responses: phytoplankton and benthic community dynamics determine the effect of an estuarine invasive suspension-feeder
Assessing toxicant effects in a complex estuary--A case study of effects of silver on reproduction in the bivalve, Potamocurbula amurensis, in San Francisco Bay
Selenium in San Francisco Bay zooplankton: Potential effects of hydrodynamics and food web interactions
Stable carbon and nitrogen isotope composition of aquatic and terrestrial plants of the San Francisco Bay estuarine system
Effects of tidal shallowing and deepening on phytoplankton production dynamics: A modeling study
Structure and flow-induced variability of the subtidal salinity field in northern San Francisco Bay
Bioavailability of organic matter in a highly disturbed Estuary: The role of detrital and algal resources
Our evolving conceptual model of the coastal eutrophication problem
Spawning, fertilization, and larval development of Potamocorbula amurensis (Mollusca: Bivalvia) from San Francisco Bay, California
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: 93Phytoplankton community ecology: Principles applied in San Francisco Bay
In his seminal 1961 paper 'The paradox of the plankton' Am Nat 95:137-147, G. E. Hutchinson asked why many species of phytoplankton can coexist while competing for a small number of limiting resources in an unstructured habitat. Hutchinson anticipated the resolution of his paradox, recognizing that communities are organized by processes beyond resource competition including species interactions, hAuthorsJ. E. Cloern, R. DuffordClimate anomalies generate an exceptional dinoflagellate bloom in San Francisco Bay
We describe a large dinoflagellate bloom, unprecedented in nearly three decades of observation, that developed in San Francisco Bay (SFB) during September 2004. SFB is highly enriched in nutrients but has low summer‐autumn algal biomass because wind stress and tidally induced bottom stress produce a well mixed and light‐limited pelagic habitat. The bloom coincided with calm winds and record high aAuthorsJ. E. Cloern, T.S. Schraga, C.B. Lopez, N. Knowles, Labiosa R. Grover, R. DugdaleDetritus fuels ecosystem metabolism but not metazoan food webs in San Francisco estuary's freshwater delta
Detritus from terrestrial ecosystems is the major source of organic matter in many streams, rivers, and estuaries, yet the role of detritus in supporting pelagic food webs is debated. We examined the importance of detritus to secondary productivity in the Sacramento and San Joaquin River Delta (California, United States), a large complex of tidal freshwater habitats. The Delta ecosystem has low prAuthorsW. V. Sobczak, J. E. Cloern, A.D. Jassby, B.E. Cole, T.S. Schraga, A. ArnsbergOne estuary, one invasion, two responses: phytoplankton and benthic community dynamics determine the effect of an estuarine invasive suspension-feeder
No abstract available.AuthorsJanet K. ThompsonAssessing toxicant effects in a complex estuary--A case study of effects of silver on reproduction in the bivalve, Potamocurbula amurensis, in San Francisco Bay
Contaminant exposures in natural systems can be highly variable. This variability is superimposed upon cyclic variability in biological processes. Together, these factors can confound determination of contaminant effects. Long term, multidisciplined studies with high frequency sampling can be effective in overcoming such obstacles. While studying trace metal contamination in the tissues of the claAuthorsCynthia L. Brown, Francis Parchaso, Janet K. Thompson, Samuel N. LuomaSelenium in San Francisco Bay zooplankton: Potential effects of hydrodynamics and food web interactions
The potential toxicity of elevated selenium (Se) concentrations in aquatic ecosystems has stimulated efforts to measure Se concentrations in benthos, nekton, and waterfowl in San Francisco Bay (SF Bay). In September 1998, we initiated a 14 mo field study to determine the concentration of Se in SF Bay zooplankton, which play a major role in the Bay food web, but which have not previously been studiAuthorsD.G. Purkerson, M.A. Doblin, S.M. Bollens, S. N. Luoma, G.A. CutterStable carbon and nitrogen isotope composition of aquatic and terrestrial plants of the San Francisco Bay estuarine system
We report measurements of seasonal variability in the C‐N stable isotope ratios of plants collected across the habitat mosaic of San Francisco Bay, its marshes, and its tributary river system. Analyses of 868 plant samples were binned into 10 groups (e.g., terrestrial riparian, freshwater phytoplankton, salt marsh) to determine whether C‐N isotopes can be used as biomarkers for tracing the originsAuthorsJ. E. Cloern, E. A. Canuel, D. HarrisEffects of tidal shallowing and deepening on phytoplankton production dynamics: A modeling study
Processes influencing estuarine phytoplankton growth occur over a range of time scales, but many conceptual and numerical models of estuarine phytoplankton production dynamics neglect mechanisms occurring on the shorter (e.g., intratidal) time scales. We used a numerical model to explore the influence of short time-scale variability in phytoplankton sources and sinks on long-term growth in an ideaAuthorsL.V. Lucas, J. E. CloernStructure and flow-induced variability of the subtidal salinity field in northern San Francisco Bay
The structure of the salinity field in northern San Francisco Bay and how it is affected by freshwater flow are discussed. Two datasets are examined: the first is 23 years of daily salinity data taken by the U.S. Bureau of Reclamation along the axis of northern San Francisco Bay; the second is a set of salinity transects taken by the U.S. Geological Survey between 1988 and 1993. Central to this paAuthorsStephen G. Monismith, Wim Kimmerer, Jon R. Burau, Mark T. StaceyBioavailability of organic matter in a highly disturbed Estuary: The role of detrital and algal resources
The importance of algal and detrital food supplies to the planktonic food web of a highly disturbed, estuarine ecosystem was evaluated in response to declining zooplankton and fish populations. We assessed organic matter bioavailability among a diversity of habitats and hydrologic inputs over 2 years in San Francisco Estuary's Sacramento-San Joaquin River Delta. Results show that bioavailable dissAuthorsW. V. Sobczak, J. E. Cloern, A.D. Jassby, A. B. Muller-SolgerOur evolving conceptual model of the coastal eutrophication problem
A primary focus of coastal science during the past 3 decades has been the question: How does anthropogenic nutrient enrichment cause change in the structure or function of nearshore coastal ecosystems? This theme of environmental science is recent, so our conceptual model of the coastal eutrophication problem continues to change rapidly. In this review, I suggest that the early (Phase I) conceptuaAuthorsJames E. CloernSpawning, fertilization, and larval development of Potamocorbula amurensis (Mollusca: Bivalvia) from San Francisco Bay, California
In Potamocorbula amurensis time for development to the straight-hinge larval stage is 48 hr at 15°C. Potamocorbula amurensis settles at a shell length of approximately 135 um 17 to 19 days after fertilization. Our observations of timing of larval development in P. amurensis support the hypothesis of earlier workers that its route of initial introduction to San Francisco Bay was as ve1iger larvae tAuthorsM.H. Nicolini, D.L. Penry - 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: