San Francisco Estuary and Watershed Science

Zooplankton density and community composition in estuaries can be affected by variation in freshwater inputs, with important implications for higher trophic levels. In the San Francisco Estuary, management agencies have initiated autumn flow augmentations in the form of changes to reservoir releases or to exported water from the South Delta to increase and improve available habitat for endangered Delta Smelt, Hypomesus transpacificus, during the season when their body condition most influences fecundity. Autumn flow augmentation only occurs in years with higher precipitation, effectively moving the Low-Salinity Zone (LSZ) downstream to key foraging habitats for Delta Smelt in Suisun Bay and Suisun Marsh. To assess whether augmented flow enhanced prey resources for Delta Smelt, we compared autumn zooplankton abundance, biomass, spatial distribution, and community composition in years when flow was augmented (2017, 2019) with reference years when flow was not augmented (2018, 2020). In augmented years, we detected higher total zooplankton abundance and altered community composition in Suisun Bay and Suisun Marsh. Increased freshwater in these regions was associated with higher abundance of Pseudodiaptomus forbesi, a preferred prey of Delta Smelt, while species associated with higher salinities—Acartiella sinensis and Tortanus dextrilobatus—were less abundant. Thus, autumn flow augmentations can influence foraging habitat and prey availability for Delta Smelt, underscoring the complex responses of estuarine zooplankton communities to changes in response to flow and salinity regimes. This study is management- relevant because it shows that important Delta Smelt prey items increase in downstream regions when X2 is lower. Whether that results in a response in Delta Smelt abundance remains to be seen.