Water-Quality in San Francisco Bay

The U.S. Geological Survey (USGS) has continuously monitored real-time water quality and suspended-sediment transport in San Francisco Bay (the Bay) since 1989 as part of a multi-agency effort (see “Acknowledgments” section) to address estuary management, water supply, and ecological concerns. The San Francisco Bay area is home to millions of people and biologically diverse marine and terrestrial flora and fauna. Freshwater mixes with saltwater in the Bay and is subject to riverine influences (floods, droughts, managed reservoir releases, and freshwater diversions) and marine influences (tides, waves, and effects of saltwater).

Water temperature, salinity, suspended-sediment concentration (SSC), and turbidity, are used by State and Federal resources managers and are monitored at eight key locations throughout the Bay (fig. 1). Water temperature and salinity affect the density of water, which controls gravity-driven circulation patterns and stratification in the water column. Salinity indicates the relative mixing of fresh and ocean waters in the Bay and is derived from specific conductance measurements. Turbidity is a measure of light scattered from suspended particles in the water that is used to estimate suspended-sediment concentration. Suspended-sediment concentrations also are directly measured through depth-integrated water sampling.

Suspended sediment affects Bay water quality in multiple ways. Suspended sediment affects phytoplankton growth by attenuating sunlight in the water column. Suspended sediment deposition on tidal marshes and intertidal mudflats helps to restore and sustain these habitats as sea level rises. Settling of suspended sediment in ports and shipping channels creates the need for more dredging. In addition, suspended sediment often carries adsorbed contaminants as it is transported in the water column, which affects the distributions and concentrations of adsorbed contaminants in the environment. Excessive concentrations of sediment-adsorbed contaminants in deposits on the bottom of the Bay can affect ecosystem health.

External factors, such as tidal currents, waves, and wind can also affect water quality in the Bay. Tidal currents in the Bay change direction four times daily, and wind direction and intensity typically fluctuate on a daily cycle. Consequently, salinity, water temperature, and suspended-sediment concentration differ spatially and temporally throughout the Bay. Therefore, high-frequency measurements at multiple locations are needed to monitor these changes. Data collected at eight stations throughout the Bay are transmitted in near real-time using cellular telemetry and posted to the USGS National Water Information System (NWIS; https://waterdata.usgs.gov/usa/nwis). The purposes of this fact sheet are to (1) provide information about the USGS San Francisco Bay water-quality monitoring network; (2) highlight various applications in which these data can be used; and (3) provide internet links to access the resulting continuous water-quality data collected by the USGS.

Program Overview

Continuous water-quality measurements are collected at eight stations in San Francisco Bay (table 1; fig. 1). Instruments are typically suspended in the water from stainless-steel cables that are anchored to the bottom of the Bay (figs. 2, 3) and are equipped with sensors that measure specific conductance, temperature, and turbidity (fig. 4A). Data are recorded every 15 minutes and are transmitted by cellular telemetry (yielding provisional data available within 1 hour of measurement) or retrieved during periodic station visits (yielding provisional data available within 1 week of the station visit). Table 1 lists the vertical location of the instruments at each station and provides the percentage of valid data collected during each instrument’s deployment during water years 2020–21 (the USGS water year runs from October 1 to September 30 and is defined by the calendar year in which the period ends). The percentage of valid data, after review and finalizing, ranged from 55 to 100 percent, with an average of 88 percent across all parameters and stations. The variability in the range of values is attributed to biological fouling and sensor failure. Biological growth (fig. 4B) affects sensor readings most frequently and usually increases with time, which requires the affected data to be revised or deleted. Copper tape is added around the instrument sensors (fig. 4A) because the copper reduces the rate and abundance of biological growth.

Each station is visited every 2–5 weeks for instrument inspection, cleaning, data retrieval, and instrument calibration as needed. Water samples are collected at the sensor depth to statistically relate turbidity data to co-located SSC (fig. 5). Periodically, discharge and cross-sectionally averaged SSC are measured concurrently at some stations to estimate the suspended-sediment flux at that location (Rasmussen and others, 2009). These data assist resource managers in quantifying the amount and direction of suspended sediment flowing in the Bay, which is necessary to understand sediment deposition. Discharge is measured using a boat-mounted acoustic Doppler current profiler (Mueller and others, 2013), and water samples are collected at several points across the channel with a depth-integrating suspended-sediment sampler (fig. 6; U.S. Geological Survey, 2006) using the equal-discharge-increment method (Edwards and Glysson, 1999). Suspended-sediment flux, expressed in mass per unit time, is computed as the product of discharge and the channel-average SSC at the indicated cross section.

Specific conductance, water temperature, and turbidity data are collected at two depths in the water column at stations featuring depths greater than 50 feet (ft) to help characterize the vertical variability in water quality. For stations in shallow water of less than 35 ft, such as San Francisco Bay at Pier 17 at San Francisco, California (table 1, USGS station number 374811122235001) and San Francisco Bay at the Northeast Shore of Alcatraz Island, California (table 1, USGS station number 374938122251801), data are collected only at one depth (U.S. Geological Survey, 2021). Specific conductance values are reported in microsiemens per centimeter (µS/cm) at 25 degrees Celsius (°C) and water temperatures reported in °C are measured using real-time smart sensors. Two types of optical sensors are used to measure turbidity values reported in formazin nephelometric units (FNU) because the YSI 6920 equipment is gradually being phased into the updated YSI EXO3 technology. In 2021, turbidity monitoring was added to the Carquinez Strait at Carquinez Bridge near Crockett, California (table 1, USGS station number 11455820).

Records undergo a thorough evaluation process before final approval. Data are analyzed, approved, and audited to ensure integrity. Data corrections (necessary because of biological fouling, sedimentation of the sensor, or instrument electronic drift) are applied to the affected periods of record following USGS guidelines (Wagner and others, 2006). Further details about these methods are available in the 2019 USGS state of the network newsletter (Work and Downing-Kunz, 2018).

Data obtained from this network have several applications, including calibrating numerical models (Bever and MacWilliams, 2013) and understanding the response of Bay water quality to extreme events such as prolonged drought (Work and others, 2017). Continuous water-quality and suspended sediment transport data, including water years 2020–21, are archived in the USGS National Water Information System (U.S. Geological Survey, 2021) and are available to the public (https://waterdata.usgs.gov/usa/nwis).