Shifts in phytoplankton productivity and community structure in the San Francisco Bay-Delta driven by Delta Outflow

Since the late 1980s, dramatic reductions in phytoplankton biomass have occurred in the San Francisco Bay-Delta. This reduction has primarily been attributed to grazing by an invasive clam and to phytoplankton growth inhibition from elevated ammonium concentrations – hence the Sacramento Regional Wastewater Treatment Plant (SRWTP) is undergoing an upgrade so it will no longer discharge ammonium. Yet, the effect of the government managed flow of water from the Sacramento-San Joaquin Delta into the San Francisco Bay (Delta Outflow) on the phytoplankton community is not well understood. Here, we present a 2015–2019 field mapping study illuminating the complex effects of Delta Outflow on phytoplankton physiology and community structure. Transects from San Pablo Bay to the Sacramento River were conducted approximately monthly on the R/V Peterson, during which photosynthetic efficiency, salinity, temperature, and light were measured continuously. At specific stations, samples were collected for phytoplankton taxonomy and nutrient analysis. The highest Delta Outflow events occurred in the winter and spring and were associated with low light availability and a turbulent, mixed water column. High Delta Outflow events were linked with low photosynthetic efficiency and an increase in cyanobacteria. As Delta Outflow subsided, thereby increasing the residence time and light availability, there was an increase in photosynthetic efficiency and phytoplankton biomass from diatoms and cryptophytes. The highest diatom concentrations tended to be localized in freshwater regions between the Sacramento River and X2, the nominal location of the 2 ppt isohaline, whereas cryptophytes were most abundant between X2 and San Pablo Bay. Changes in ammonium concentrations did not have a significant effect on the phytoplankton biomass – thus, the future SRWTP upgrade is unlikely to have a dramatic effect either. These results demonstrate that the multitude of physiochemical changes resulting from Delta Outflow events can markedly alter phytoplankton productivity in the Bay-Delta.