Sampling Methods for the Water Quality of San Francisco Bay Project

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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.

What We Measure and How Our Measurements Are Made

The  goal of the Water Quality of San Francisco Bay Research and Monitoring Project is to measure and understand how estuarine systems and tidal river deltas function and change in response to hydro-climatic variability and human activities. This project is designed to measure changes in water quality along the deep channel of the San Francisco Bay-Delta system. We conduct monthly cruises on the R/V David H. Peterson along a transect of fixed stations, collecting a core set of measurements that fall into two categories:

  1. Submersible sensors to measure vertical profiles of salinity, temperature, chlorophyll fluorescence, dissolved oxygen, turbidity, and photosynthetically active radiation
  2. Discrete water samples to measure chlorophyll-a, dissolved oxygen, suspended particulate matter (SPM), and dissolved inorganic nutrients

Submersible Sensors

Example of a Conductivity, Temperature, and Depth instrument package used to monitor water quality in the San Francisco Bay.

A Conductivity, Temperature, and Depth (CTD) instrument package, which uses specialized sensors to measures multiple water quality parameters.

Vertical profiles of water quality data are collected using a submersible Conductivity, Temperature, and Depth (CTD) instrument package. The CTD concurrently measures multiple water quality parameters with specialized sensors as shown in the adjacent photo. The sensors make 5-24 measurements per meter as the CTD is lowered through the water column.

From CTD sensors we derive measurements of depth, calculated chlorophyll-a, dissolved oxygen, oxygen percent saturation, calculated suspended particulate matter (SPM), light extinction coefficient, salinity, temperature, and sigma-t.  Each of these parameters is described in our glossary.

 

Discrete Water Samples

Discrete water samples are collected at a subset of stations and analyzed for chlorophyll-a, SPM, dissolved oxygen, and dissolved inorganic nutrients (nitrite , nitrate + nitrite, ammonium, phosphate, and silicate). The discrete chlorophyll-a and SPM are used to calibrate the fluorometer and optical backscatter sensor (OBS) on the CTD. 

For each cruise we use linear regressions of the discrete measurements and sensor volts to estimate concentrations at stations and depths where discrete samples are not collected. The discrete chlorophyll-a versus chlorophyll fluorescence regression is used to calculate chlorophyll-a concentrations, and the discrete SPM versus OBS regression is used to calculate SPM concentrations at all stations and depths where the CTD is deployed (see adjacent example photo).  

Example of a typical discrete chlorophyll-a vs. CTD fluorometer regression

A typical discrete chlorophyll-a vs. CTD fluorometer regression plot. The resulting linear regression equation is used to calculate Chlorophyll-a from fluorescence measurements.

Discrete water samples are collected at two depths: (1) near surface (~2 meters) using a fixed flow-through pump installed in the bow of the vessel, and (2) near bottom using a Niskin sampler. Discrete samples are currently collected at stations 36, 32, 30, 27, 24, 22, 18, 15, 13, 9, 6, 3, 649, and 657 with extra samples added as needed for the regressions described above.

Our entire sensor and discrete dataset is available for download from the Data Query for the Water Quality of San Francisco Bay Project Page, along with a glossary that describes each of the parameters. Our dataset is also stored in two data reports for 1969-2015 and 2016-present.

As technology and our research project goals evolve, so do the parameters we sample, and technology we employ on our cruises. The complete historical methodology and technical validations are shared in Water quality measurements in San Francisco Bay by the U.S. Geological Survey, 1969–2015.

 

Phytoplankton Community Composition

The taxonomic composition of the phytoplankton community affects the health of the ecosystem, influencing numerous aspects from the quality of phytoplankton as a food resource for consumers, to the potential for harmful algal blooms. We collect discrete surface water samples at a subset of stations along the salinity gradient for analysis of phytoplankton taxonomy and biomass. These data along with descriptions of sampling and analytical methods are available in two data reports for 1992-2014 and 2014-present.