An Investigation of Factors Affecting the Decline of Delta Smelt (Hypomesus transpacificus) in the Sacramento-San Joaquin Estuary

The delta smelt is an annual fish that is endemic to the Sacramento-San Joaquin Estuary and is protected under federal and California Endangered Species Acts. Record low abundances have occurred since 2004. Three questions are addressed here: What is the relative importance of environmental factors with direct effects on abundance? Do factors that may have indirect effects provide an explanation of abundance changes? Are effects of environmental factors better accounted for individually or as criteria defining the volume of water with suitable abiotic attributes? Strong evidence was found of density-dependent population regulation. The density of prey was the most important environmental factor explaining variations in delta smelt abundance from 1972 to 2006 and over the recent period of decline in the abundance of the fish. Predation and water temperature showed possible effects. Entrainment of delta smelt at south Delta pumping plants showed statistically significant effects on adult-to-juvenile survival but not over the fish's life cycle. Neither the volume of water with suitable abiotic attributes nor other factors with indirect effects, including the location of the 2 ppt isohaline in the Delta in the previous fall (“fall X2”), explained delta smelt population trends beyond those accounted for by prey density. [Supplementary materials are available for this article. Go to the publisher's online edition of Reviews in Fisheries Science for the following free supplemental resources: information on factor selection and specification; and estimating the volume of abiotic habitat.]