Data Query for the Water Quality of San Francisco Bay Project

Welcome to the San Francisco Bay water quality database containing measurements collected from 1969 to present as part of the San Francisco Bay research program.

This dataset consists of discrete parameters: chlorophyll-a, suspended particulate matter (SPM), dissolved oxygen, and dissolved inorganic nutrients (nitrite, nitrate + nitrite, ammonium, phosphate and silicate) and CTD sensor-derived parameters: depth, calculated chlorophyll-a, dissolved oxygen, oxygen % saturation, calculated SPM, extinction coefficient, salinity, temperature, and sigma-t.

Each parameters is described in our Glossary. Please see what we measure and how our measurements are made for more details. Detailed information about the measurements, historical methodology, and technical validations can be found in Water quality measurements in San Francisco Bay by the U.S. Geological Survey, 1969–2015. Database data in spreadsheet form are accessible in these publications for 1969-2015 and 2016-2021.

To access phytoplankton taxonomy data see these data reports: 1992-2014 and 2014-present.

Database Structure

From 1969 through October 1987, discrete parameters were collected at varying depths (commonly 0.5m, 1m, 2m, 5m, and bottom) and extinction coefficient is listed at 0.5m, 1m or 2m.

From November 1987 to present, discrete data are collected at a subset of stations at 2m and/or the station’s bottom depth. Extinction coefficient is listed on the 1m line, or the surface depth if 1m bin was not sampled by CTD.

CTD sampling: From November of 1987 to present, vertical CTD profile data are shared in 1-m depth bins centered at the depth reported; the values are means of all measurements made 0.5 m above and 0.5 m below the reported depth.

Known data limitations

The following data are not available: silicate 2011 - February 2014; nitrite 2005 – 2011; extinction coefficient 2002 – 2006

Time of day for 1981 through 1987 is accurate within +/- 30 minutes.

There are intermittent periods where we did not have specific parameters, reach out to Erica Nejad ( with any questions.

Database Query

Selection by year: Select a year from the menu below in order to load all of the cruise data for that year into the table (the current year is shown by default). Please wait a moment after selecting the year for your data to become visible in the table. Once the data are visible, you can click on the Date, Julian Date, or Station headers to sort by one of those columns.

Selection by cruise: Once you have chosen a year, click on a cruise date in the Date column to load all data for a single cruise. The "Show all data" link above the table will return you to that full year's data.

Selection of full(er) dataset: The 1969-2015 data are available as a single file from this data release and the 2016-2021 data are available as a single file from this data release.

Data Visualizations: When a single cruise is selected, interpolations of chlorophyll, salinity, temperature, SPM, and dissolved oxygen data are displayed below the data table. The interpolations were created from vertical profile sensor data collected at the fixed sample stations. Each color image shows the longitudinal and vertical distributions of a single parameter, dark hues represent high concentrations and light hues represent low concentrations. Color variations from left to right represent longitudinal variability of the parameter. Color variations from top to bottom show the vertical variability from the water surface to the bottom. The black outline below shows the shape of the Bay floor.

For an explanation of parameters used in the database, please see our glossary (opens in a new tab).

Click the Export as CSV button to download the selected data. All data selected and in the table will be exported, regardless of how many entries are visible on the page.

For any publications, please cite these data using the citations at the bottom of this page.

Contact Erica Nejad ( with database questions.

Current Data Availability: All except nutrient data: April 10, 1969 - December 6, 2023. Nutrient Data: April 10, 1969 - December 6, 2023

Select a Year:

Date Julian Date Time Station Distance from Sta. 36 (km) Depth (m) Discrete Chlorophyll-a (micrograms/L) Discrete Chlorophyll-Pheopigment Ratio Calculated Chlorophyll-a (micrograms/L) Discrete Oxygen (mg/L) Oxygen (mg/L) Oxygen % Saturation Discrete SPM (mg/L) Calculated SPM (mg/L) Extinction Coefficient Salinity Temperature (Degrees Celsius) Sigma-t NO2 (Micromolar) NO32 (Micromolar) NH4 (Micromolar) PO4 (Micromolar) Si (Micromolar)

Data Citation

Please use these citations to cite data from this website in your publication:

Data from 2022 and after must be considered preliminary. 2022 citation expected by December 2023.

Data from 2016-2021:

Schraga, T.S., Nejad, E.S., Martin, C.A., and Cloern, J.E., 2018, USGS Measurements of Water Quality in San Francisco Bay (CA), 2016-2021 (ver. 4.0, March 2023): U.S. Geological Survey data release,

Data from 1969-2015:

Schraga, T. S. & Cloern, J. E., 2017, Water quality measurements in San Francisco Bay by the U.S. Geological Survey, 1969–2015. Sci. Data 4:170098 doi 10.1038/sdata.2017.98.

Cloern, J.E., and Schraga, T.S., 2016, USGS Measurements of Water Quality in San Francisco Bay (CA), 1969-2015 (ver. 4.0, March 2023): U. S. Geological Survey data release,