Evaluating the effects of wastewater-derived nutrients on phytoplankton abundance and community structure in the San Francisco Estuary and Delta

Science Center Objects

Planned upgrades to the Sacramento Regional wastewater treatment plant (SRWTP) will substantially reduce nutrient discharge and also alter the types and amounts of nutrients being distributed across the San Francisco Delta and Estuary (Delta).

One highly anticipated outcome of lower nutrients is improved productivity in the phytoplankton communities that supply aquatic food webs, which should improve conditions for declining pelagic fish species. Reductions in the occurrence of harmful algal blooms and associated cyanotoxins is another possible beneficial outcome of the planned upgrades.

Assessing the relationships between the distribution of nutrients and phytoplankton under different conditions across the Delta is the best means to understand how managing nutrient supplies affects aquatic food webs. Knowing more about how nutrient management affects aquatic food webs will help managers evaluate the potential environmental benefits of future nutrient reduction efforts against the costs.

This project will evaluate the effects of wastewater-derived nutrients on the phytoplankton community by employing three complementary approaches.

USGS scientists conduct boat-based mapping survey

USGS scientists conduct boat-based mapping survey

Boat-based Mapping Survey

The first approach is a novel high-resolution, boat-based mapping survey system that provides spatial information over large regions for a specific time period (e.g. 4 consecutive days of data collection). This produces, for example, high-resolution maps of ammonium, nitrate, phytoplankton abundance, phtytoplankton community composition, and water quality (temperature, specific conductance, turbidity, dissolved oxygen, etc.).

Continuous Monitoring Stations

In the second approach, the USGS will enhance existing continuous monitoring stations in the Delta, making them capable of monitoring not only phytoplankton abundance but also the types of phytoplankton present in the water column. This data will be available every 15 minutes in real time, producing a continuous times series of data to permit examination of any changes over time.

Intensive Sampling

The third approach will be to collect discrete samples during the mapping surveys at approximately 30 locations across the Delta and at the continuous monitoring stations at least monthly. These samples will be analyzed for nitrate, ammonium, phosphate, total dissolved nitrogen, dissolved organic carbon, chlorophyll-a, phaeophytin, phytoplankton enumeration, picoplankton direct counts, and cyanotoxins.

bluegreen algae distribution map

Preliminary results of survey conducted July 27 and 28, 2020 showing distribution of bluegreen algae. These and other preliminary project results are available on the DATA/TOOLS tab.


The timeline for the collection of data will span from the spring of 2020 to the fall of 2021. Over the course of the study, both mapping survey data and data collected at fixed stations will be shared as it becomes available. A synthesis of study results will be presented at conferences and stakeholder meetings as appropriate. Final data from the mapping surveys will be published as a product on the USGS Science Base data repository, and data from the fixed stations published on NWIS.  We will also make the data analysis and visualization tools we use for preparation of the synthesis publicly available online together with the data to make it possible for stakeholders, researchers and managers to explore the data themselves and download portions for further analysis.