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Water Quality of San Francisco Bay Research and Monitoring Project Active

By California Water Science Center August 3, 2020

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

 

Our Science in the News

 

Agencies Supporting the Program of Water-Quality Data Collection and Dissemination

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.

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Map showing current San Francisco Bay-Delta water quality sampling station locations.

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.
By
Water Resources Mission Area, California Water Science Center
link

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.
Learn More
link
Scientist sample for clams aboard the R/V Polaris in North San Francisco Bay.

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.
By
Water Resources Mission Area, California Water Science Center
link

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.
Learn More
link
R/V David H. Peterson at the Redwood City dock.

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.
By
Water Resources Mission Area
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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.
Learn More

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 w
By
Water Resources Mission Area

Phytoplankton 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
By
Water Resources Mission Area

Below are multimedia items associated with the Water Quality of San Francisco Bay project.

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PubTalk 7/2011 — How is San Francisco Bay Doing?
video thumbnail: Delta Science: Excerpt from “Delta Revival” link
Delta Science: Excerpt from “Delta Revival”

Below are publications associated with the Water Quality of San Francisco Bay project.

Filter Total Items: 93

Patterns, 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 m
Authors
James Cloern
By
Water Resources Mission Area

Blurred 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 routine
Authors
Melissa B. Peacock, Corinne M. Gibble, David B. Senn, James E. Cloern, Raphael M. Kudela
By
Water Resources Mission Area

Why 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 domin
Authors
James E. Cloern
By
Water Resources Mission Area

The 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 a
Authors
Monika Winder, Jacob Carstensen, Aaron W.E. Galloway, Hans H. Jakobsen, James E. Cloern
By
Water Resources Mission Area

How 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 Francisc
Authors
Fernanda Achete, Mick Van der Wegen, Jan Adriaan Roelvink, Bruce E. Jaffe
By
Pacific Coastal and Marine Science Center

Application 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 suit
Authors
R.C. Martyr-Koller, H.W.J. Kernkamp, Anne A. Van Dam, Mick van der Wegen, Lisa Lucas, N. Knowles, B. Jaffe, T.A. Fregoso
By
Water Resources Mission Area, San Francisco Bay and Sacramento-San Joaquin Delta Estuary

Ecosystem 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., sil
Authors
James E. Cloern, Alan D. Jassby, Tara Schraga, Erica S. Kress, Charles A. Martin
By
Water Resources Mission Area, San Francisco Bay and Sacramento-San Joaquin Delta Estuary

Bivalve 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 phytoplankton
Authors
Lisa Lucas, James E. Cloern, Janet K. Thompson, Mark T. Stacey, Jeffrey K. Koseff
By
Water Resources Mission Area, San Francisco Bay and Sacramento-San Joaquin Delta Estuary

Human 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 dev
Authors
James 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 Yin
By
Water Resources Mission Area

Unintended 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 Projec
Authors
John 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. Athearn
By
Ecosystems Mission Area, Contaminant Biology, Environmental Health Program, Forest and Rangeland Ecosystem Science Center, Western Ecological Research Center (WERC)

Phytoplankton 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 blo
Authors
Jacob Carstensen, Riina Klais, James E. Cloern
By
Water Resources Mission Area, San Francisco Bay and Sacramento-San Joaquin Delta Estuary

A 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 enablin
Authors
F. M. Achete, M. van der Wegen, D. Roelvink, B. Jaffe
By
Pacific Coastal and Marine Science Center

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.

By
Water Resources Mission Area, California Water Science Center