Understanding how natural and human‐induced processes interact to influence ecosystem responses is essential for their effective management and conservation. Long‐term environmental degradation of the upper San Francisco Estuary, California, has resulted in numerous species declines. In this study, we used pelagic fish monitoring and hydrodynamic data during winter–spring 2002–2014 to evaluate how natural and human‐induced environmental changes in the upper San Francisco Estuary may have influenced the distribution, abundance, and community structure of the pelagic fishes. Delta outflow and turbidity tended to decline and salinity tended to increase since the early 2000s. Twelve of the 27 pelagic fish species sampled were introduced, most of which were freshwater‐dominant species in highly altered upstream areas. Overall mean relative abundance was similar between native and introduced fishes across all study areas. The upstream distribution of the eight most abundant pelagic fishes was generally associated with their salinity habitat components. Among these species, the Delta Smelt Hypomesus transpacificus and the introduced Threadfin Shad Dorosoma petenense had the highest rates of population decline over the period 2002–2014 and the largest relative increase in salinity predicted in their habitats due to hydrological alteration. Community structure was significantly related to abiotic factors (water temperature, salinity, and turbidity) and spatiotemporal variation (longitude and month), which accounted for 30–33% of the variation. Low to intermediate outflows due to droughts and water diversions since the early 2000s likely interacted synergistically with multiple factors, decreasing the abundance of several pelagic species. Management actions linking ecologic, hydrologic, and geomorphic processes with multiple stressors could help to reverse the long‐term decline of Delta Smelt and other threatened and endangered fishes in the San Francisco Estuary.

Understanding reproductive biology and performance of fish is essential to formulate effective conservation and management programs. Here, we studied reproductive strategies of female Delta Smelt Hypomesus transpacificus, an endangered fish species in the State of California, the United States, focusing on (1) better understanding their distribution pattern during the winter and spring spawning season at very fine scale to predict their possible spawning grounds and (2) assessing impacts of a recent, severe drought on their reproductive performance. We formulated our hypotheses as follows; (1) female Delta Smelt migrate to particular locations for spawning so that mature females can be frequently found in those locations throughout the spawning season and (2) reproductive performance of individual female fish declined during the drought. To test the first hypotheses, we analyzed relationships between water quality parameters and maturity/distribution pattern of Delta Smelt. Salinity better explained the distribution pattern of Delta Smelt at subadult and adult stages compared with water temperature or turbidity. Although there are some freshwater locations where mature Delta Smelt can frequently be found during the spawning season, Delta Smelt at the final maturation stage (Stage 5: hydration) and post spawners appeared to be widespread in the area where salinity was below 1.0 during the spawning season. Therefore, Delta Smelt could theoretically spawn in any freshwater locations, with more specific spawning requirements in the wild (e.g., substrate type and depth) still unknown. Delta Smelt, which experienced dry and critically dry conditions (the 2013 and 2014 year-classes), showed smaller oocytes, and lower clutch size and gonadosomatic index compared with the fish caught in a wet year (2011 year-class) at the late vitellogenic stage (Stage 4 Late), suggesting reproductive performance was negatively affected by environmental conditions during the drought.

The San Fransisco Estuary is an important nursery for young fish. Scientists use special nets and techniques to identify and count small fish in the estuary. Knowing how many and where the young fish are helps managers avoid harm to fish populations. Water flowing in rivers naturally flows out to sea, but in the San Francisco Estuary, some of that water is stored in reservoirs or pumped to other parts of California, which can have a negative impact on fish populations. These and other challenges to fish have resulted in severe declines in numerous species. In this article we will describe how we monitor young fish population trends. We also describe how the sampling method changes depending on the habitat and time of year sampling occurs. Finally, we explain how the information is used by scientists, managers, and the public within the San Francisco Estuary, California, USA.