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.
Sampling Locations for the Water Quality of San Francisco Bay Project
Sampling Methods for the Water Quality of San Francisco Bay Project
Research Vessel David H. Peterson
Directly measured parameter data (depth, chlorophyll-a, dissolved oxygen, suspended particulate matter, extinction coefficient, salinity, temperature, nutrients) are available from the locations below:
USGS Measurements of Water Quality in San Francisco Bay (CA), 2016-2021 (ver. 4.0, March 2023)
Phytoplankton Species Composition, Abundance and Cell Size in San Francisco Bay: Microscopic Analyses of USGS Samples Collected 1992-2014
Below are publications associated with the Water Quality of San Francisco Bay project.
Patterns, pace and processes of water-quality variability: Examples from a long-studied estuary
Blurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California
Why large cells dominate estuarine phytoplankton
The land-sea interface: A source of high-quality phytoplankton to support secondary production
How can climate change and engineered water conveyance affect sediment dynamics in the San Francisco Bay-Delta system?
Application of an unstructured 3D finite volume numerical model to flows and salinity dynamics in the San Francisco Bay-Delta
Ecosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay
Bivalve grazing can shape phytoplankton communities
Human activities and climate variability drive fast-paced change across the world's estuarine-coastal ecosystems
Unintended consequences of management actions in salt pond restoration: cascading effects in trophic interactions
Phytoplankton blooms in estuarine and coastal waters: Seasonal patterns and key species
A 2-D process-based model for suspended sediment dynamics: A first step towards ecological modeling
Directly measured parameter data (depth, chlorophyll-a, dissolved oxygen, suspended particulate matter, extinction coefficient, salinity, temperature, nutrients) are available from the locations below:
Data Query for the Water Quality of San Francisco Bay Project
Since 1969, USGS has collected water-quality data along the deep-channel longitudinal axis of the San Francisco Bay-Delta system at 37 fixed locations spaced 3-6 kilometers apart. The Water Quality of San Francisco Bay Data Query provides access to the entire dataset.
- 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.
Sampling Locations for the Water Quality of San Francisco Bay Project
Since 1969, the Water Quality of San Francisco Bay Research and Monitoring Project has conducted water-column sampling along the deep channel of the San Francisco Bay-Delta system. Learn more about when and where we collect data.Sampling Methods for the Water Quality of San Francisco Bay Project
The Water Quality of San Francisco Bay Research and Monitoring Project measures changes in water quality along the deep channel of the San Francisco Bay-Delta system using submersible sensors and discrete water samples. Learn more about how we collect and measure water-quality data.Research Vessel David H. Peterson
The Research Vessel David H. Peterson begain service with the U.S. Geological Survey in 2015. Named after a founder of the Water Quality of San Francisco Bay Research and Monitoring Project, this vessel is a high-tech scientific platform for estuarine research. Learn more about how the R/V David H. Peterson makes our research possible. - Data
Directly measured parameter data (depth, chlorophyll-a, dissolved oxygen, suspended particulate matter, extinction coefficient, salinity, temperature, nutrients) are available from the locations below:
USGS Measurements of Water Quality in San Francisco Bay (CA), 2016-2021 (ver. 4.0, March 2023)
The U.S. Geological Survey maintains a program of water-quality studies in San Francisco Bay (CA) that began in 1969. This U.S.G.S. Data Release is a continuation of the previously published 1969-2015 dataset (Cloern and Schraga, 2016; Schraga and Cloern, 2017), it will archive and make available all measurements from 2016 and thereafter. Each year, a data file containing the previous years data wPhytoplankton Species Composition, Abundance and Cell Size in San Francisco Bay: Microscopic Analyses of USGS Samples Collected 1992-2014
This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from April 1992 through March 2014. Phytoplankton samples were collected at 31 stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmental - Multimedia
- Publications
Below are publications associated with the Water Quality of San Francisco Bay project.
Filter Total Items: 93Patterns, pace and processes of water-quality variability: Examples from a long-studied estuary
Environmental time series have rich information content that is invaluable for measuring and understanding changes over time and guiding policies to manage change. I extracted information from measurements of 10 water‐quality constituents in upper San Francisco Bay from 1975 to 2016, one of the longest observational records in a U.S. estuary. Changes were detected at every time scale captured by mAuthorsJames CloernBlurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California
San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are few commercial fishery harvests within SFB, recreational and subsistence harvesting for shellfish is common. Coastal shellfish are monitored for domoic acid and paralytic shellfish toxins (PSTs), but within SFB there is no routineAuthorsMelissa B. Peacock, Corinne M. Gibble, David B. Senn, James E. Cloern, Raphael M. KudelaWhy large cells dominate estuarine phytoplankton
Surveys across the world oceans have shown that phytoplankton biomass and production are dominated by small cells (picoplankton) where nutrient concentrations are low, but large cells (microplankton) dominate when nutrient-rich deep water is mixed to the surface. I analyzed phytoplankton size structure in samples collected over 25 yr in San Francisco Bay, a nutrient-rich estuary. Biomass was dominAuthorsJames E. CloernThe land-sea interface: A source of high-quality phytoplankton to support secondary production
Coastal-estuarine systems are among the most productive marine ecosystems and their special role in producing harvestable fish and shellfish has been attributed to high primary production fueled by nutrient runoff from land and efficient trophic transfer. Here we ask if phytoplankton species composition and their food quality based on the percentage of long-chain essential fatty acids (LCEFA) is aAuthorsMonika Winder, Jacob Carstensen, Aaron W.E. Galloway, Hans H. Jakobsen, James E. CloernHow can climate change and engineered water conveyance affect sediment dynamics in the San Francisco Bay-Delta system?
Suspended sediment concentration is an important estuarine health indicator. Estuarine ecosystems rely on the maintenance of habitat conditions, which are changing due to direct human impact and climate change. This study aims to evaluate the impact of climate change relative to engineering measures on estuarine fine sediment dynamics and sediment budgets. We use the highly engineered San FranciscAuthorsFernanda Achete, Mick Van der Wegen, Jan Adriaan Roelvink, Bruce E. JaffeApplication of an unstructured 3D finite volume numerical model to flows and salinity dynamics in the San Francisco Bay-Delta
A linked modeling approach has been undertaken to understand the impacts of climate and infrastructure on aquatic ecology and water quality in the San Francisco Bay-Delta region. The Delft3D Flexible Mesh modeling suite is used in this effort for its 3D hydrodynamics, salinity, temperature and sediment dynamics, phytoplankton and water-quality coupling infrastructure, and linkage to a habitat suitAuthorsR.C. Martyr-Koller, H.W.J. Kernkamp, Anne A. Van Dam, Mick van der Wegen, Lisa Lucas, N. Knowles, B. Jaffe, T.A. FregosoEcosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay
The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silAuthorsJames E. Cloern, Alan D. Jassby, Tara Schraga, Erica S. Kress, Charles A. MartinBivalve grazing can shape phytoplankton communities
The ability of bivalve filter feeders to limit phytoplankton biomass in shallow waters is well-documented, but the role of bivalves in shaping phytoplankton communities is not. The coupled effect of bivalve grazing at the sediment-water interface and sinking of phytoplankton cells to that bottom filtration zone could influence the relative biomass of sinking (diatoms) and non-sinking phytoplanktonAuthorsLisa Lucas, James E. Cloern, Janet K. Thompson, Mark T. Stacey, Jeffrey K. KoseffHuman activities and climate variability drive fast-paced change across the world's estuarine-coastal ecosystems
Time series of environmental measurements are essential for detecting, measuring and understanding changes in the Earth system and its biological communities. Observational series have accumulated over the past 2–5 decades from measurements across the world's estuaries, bays, lagoons, inland seas and shelf waters influenced by runoff. We synthesize information contained in these time series to devAuthorsJames E. Cloern, Paulo C. Abreu, Jacob Carstensen, Laurent Chauvaud, Ragnar Elmgren, Jacques Grall, Holly Greening, John O.R. Johansson, Mati Kahru, Edward T. Sherwood, Jie Xu, Kedong YinUnintended consequences of management actions in salt pond restoration: cascading effects in trophic interactions
Salt evaporation ponds have played an important role as habitat for migratory waterbirds across the world, however, efforts to restore and manage these habitats to maximize their conservation value has proven to be challenging. For example, salinity reduction has been a goal for restoring and managing former salt evaporation ponds to support waterbirds in the South Bay Salt Pond Restoration ProjecAuthorsJohn Y. Takekawa, Joshua T. Ackerman, Arriana Brand, Tanya R. Graham, Collin A. Eagles-Smith, Mark P. Herzog, Brent R. Topping, Gregory Shellenbarger, James S. Kuwabara, Eric Mruz, Sara L. Piotter, Nicole D. AthearnPhytoplankton blooms in estuarine and coastal waters: Seasonal patterns and key species
Phytoplankton blooms are dynamic phenomena of great importance to the functioning of estuarine and coastal ecosystems. We analysed a unique (large) collection of phytoplankton monitoring data covering 86 coastal sites distributed over eight regions in North America and Europe, with the aim of investigating common patterns in the seasonal timing and species composition of the blooms. The spring bloAuthorsJacob Carstensen, Riina Klais, James E. CloernA 2-D process-based model for suspended sediment dynamics: A first step towards ecological modeling
In estuaries suspended sediment concentration (SSC) is one of the most important contributors to turbidity, which influences habitat conditions and ecological functions of the system. Sediment dynamics differs depending on sediment supply and hydrodynamic forcing conditions that vary over space and over time. A robust sediment transport model is a first step in developing a chain of models enablinAuthorsF. M. Achete, M. van der Wegen, D. Roelvink, B. Jaffe - 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:
Data Query for the Water Quality of San Francisco Bay Project
Since 1969, USGS has collected water-quality data along the deep-channel longitudinal axis of the San Francisco Bay-Delta system at 37 fixed locations spaced 3-6 kilometers apart. The Water Quality of San Francisco Bay Data Query provides access to the entire dataset.