High Speed Mapping of Nutrient Distributions and Water Quality Survey - Lower South San Francisco Bay

Science Center Objects

This project aims to characterize spatial heterogeneity for key water quality parameters, and pilot the use of underway-flowthrough mapping of biogeochemical properties as a cost-effective approach to monitoring. 

Study location map of the lower South San Francisco Bay (red transect lines) and sloughs (green transect lines).

Study location map of the lower South San Francisco Bay (red transect lines) and sloughs (green transect lines). Suggested discrete sample collection sites are shown in the lower South Bay (red circles) and in the sloughs (green circles) for verification of the flowthrough instrumentation. Spatial mapping in the Lower South Bay, following the red transect lines are suggested as examples only, as ability to follow these transect liness depend on the tides. In the Bay, the extreme outside points are highly susceptible to low tide, where these areas become sub to intertidal mud flats. The ability to provide spatial maps in the sloughs (green transect lines) will also be dependent on the tides (water depths can be less than 0.1 m).

(Public domain.)

The recent nutrient conceptual model report for San Francisco Bay (SFEI, 2014) identified the need for higher spatial and temporal resolution water quality data to inform condition assessment and calibrate water quality models. This project aims to characterize spatial heterogeneity for key water quality parameters, and pilot the use of underway-flowthrough mapping of biogeochemical properties as a cost-effective approach to monitoring. The project will also yield important water quality data at high spatial resolution for multiple habitats in Lower South Bay (LSB; south of Dumbarton Bridge) that will provide important information that complement data collection in other on-going mechanistic and monitoring studies in LSB (Figure 1). The work will be carried out using a boat equipped with a suite of in-situ sensors designed to measure high frequency, continuous water quality data via a suite of flowthrough sensors that have been successfully applied for high resolution mapping in the Delta.

LSB was selected as the focus area for this initial study because it is characterized by strong spatial gradients of water quality properties. Focusing monitoring program development projects and mechanistic studies in LSB (and South Bay) is a wise investment of science resources, because the large spatial gradients in water quality parameters will most rapidly and efficiently yield important knowledge that can be transferred to studies in other subembayments. We expect the approach being explored in this project will be broadly applicable to other areas of the Bay, and could become a valuable component of future monitoring. Open-Bay areas of LSB have the highest nutrient concentrations and phytoplankton biomass in San Francisco Bay. Based on limited data attained to date, this region of the Bay also appears to have some of the largest spatial gradients of water quality properties. For example, recent data from moored sensors indicate that some sloughs have substantially higher phytoplankton biomass (e.g., up to 10 times higher than measured at Dumbarton Bridge), and commonly experience low DO (< 5 mg/L, and commonly <2-3 mg/L) for extended periods of time (SFEI, 2014). Although nutrients are not routinely monitored in most sloughs and creek habitats, existing data suggest that dissolved inorganic nitrogen and dissolved inorganic phosphorous concentrations in Coyote Creek are 3-5 times and 2-3 times higher, respectively, than concentrations at open-Bay stations in LSB (Lower South Bay Synthesis, SFEI 2015). Some sloughs are in hydraulic communication with restored salt ponds. The extent to which these connections influence slough, creek, and open-Bay water quality and phytoplankton are poorly known. However, moored sensor DO and chl-a data from Dumbarton Bridge suggest that exchange with margin habitats has a strong influence on water quality. Strong gradients of phytoplankton biomass and physical (e.g. light, temperature, mixing regime) and chemical (nutrients) conditions could lead to commensurate gradients in phytoplankton community composition. In fact, one working hypothesis is that restored salt ponds serve as incubators for potentially harmful algal species (SFEI, 2014). This project addresses the ecosystem and climate strategic directions in the USGS Science Plan, for example 'Understanding Ecosystems and Predicting Ecosystem Change' as well as 'Climate Variability and Change' (U.S. Geological Survey, 2007). This is accomplished by improving our understanding of how biogeochemical variables are distributed from the sloughs to the Lower South Bay. Understanding these variables over time also leads to a better understanding of the effects of freshwater flow and climate.

Objectives of this project are as follows:

  1. Assess the feasibility and effectiveness of using surface water mapping (coupled with discrete samples) to characterize water quality for a range of parameters in LSB.
  2. Evaluate spatial heterogeneity, and assess the need for and/or benefit of using this approach as a component of routine monitoring in LSB and other subembayments.
  3. Perform the first high spatial resolution characterization of sloughs and creeks in LSB.
  4. Characterize water quality in LSB open Bay, sloughs, and creeks under different tidal regimes (flood and ebb tide; neap and spring tides), and during several periods that are expected to have very different conditions (spring, early summer, late summer, fall). The spatial mapping data will be interpreted alongside data from continuous moored sensors at fixed stations throughout LSB to develop a system-scale biogeochemical picture.