San Francisco Estuary and Watershed Science

Phytoplankton subsidies from river inputs and wetland habitats can be important food sources for pelagic organisms in the Sacramento–San Joaquin Delta (Delta). However, while the Sacramento River is a key contributor of water to the Delta, providing 80% of the mean annual inflow, the river is only a minor source of phytoplankton to the system. The reason for low phytoplankton biomass in the Sacramento River is not well understood but appears to be associated with a 65-km stretch of the lower river where chlorophyll-a (Chl-a) concentrations can decline by as much as 90%. We conducted two surveys along the lower Sacramento River, in spring and fall of 2016, to investigate the relative contributions of different factors potentially driving this Chl-a decline. Our study evaluated the change in Chl-a concentrations as a result of dilution from tributaries, light availability, nutrient concentrations, nutrient uptake, phytoplankton productivity, zooplankton grazing, and clam grazing. Chl-a concentration decreased from 14 µg/L to 1.8 µg/L in the spring and from 4.0 µg/L to 1.2 µg/L in the fall. Dilutions from the Feather River and American River contributed 39% and 11% of Chl-a declines, respectively, during the spring. Average water depths roughly doubled downstream of the American River confluence, reducing water column light availability and lowering productivity. Zooplankton and clam grazing rates were generally low. Using a mass balance analysis, the measured variables explained 76% of the observed decline in Chl-a in the spring, suggesting additional losses from unidentified factors. We found that phytoplankton biomass is regulated by multiple potential factors in the lower Sacramento River, emphasizing the need for practitioners of restoration and management programs to evaluate multiple potential loss factors when attempting to enhance phytoplankton production in the Delta, or other large river systems.