Factors controlling calanoid copepod biomass and distribution in the upper San Francisco estuary and implications for managing the imperiled delta smelt

The tiny crustaceans referred to as copepods comprise the prey, the main food source, for delta smelt. The lack of copepods in certain areas of the Delta and at certain times in much of the Delta is a primary factor limiting the abundance of delta smelt. It has been assumed that increased flows though the Delta should bring food into areas occupied by delta smelt; however the supply of food to the fish is determined by multiple factors, such as the number of copepods already in an area, availability of certain nutrients, water temperature and clarity, and copepod residence time, that is, how long copepods may stay in suitable ambient conditions when they encounter them. A management question arises — can we manipulate outflows through the Delta to increase food supplies for delta smelt?  The question is complex because flows influence both the factors that affect copepod abundance and their distribution; that is, outflow sometimes move copepods towards delta smelt and sometimes away from them. By developing a model to explain copepod abundance at different times and places in the Delta, we were able to simulate the effects of changes in outflow on delta smelt prey. We found that increasing flows through the Delta in the autumn of years experiencing greater precipitation, a management action in both the 2008 and 2019 Biological Opinions intended by the US Fish and Wildlife Service to benefit delta smelt, actually made prey availability worse for delta smelt. That food is mobilized into areas of the Delta that offer poorer habitat conditions for delta smelt. Alternatively, increasing outflow during the spring of drier years appears to improve food conditions in areas that offer seasonally better habitat conditions and are frequently occupied delta smelt.

Hamilton SA, Bartell SM, Pierson JJ, Murphy DD. 2020. Factors controlling calanoid copepod biomass and distribution in the upper San Francisco Estuary and implications for managing the imperiled delta smelt (Hypomesus transpacificus). Environmental Management 65:587-601.