The San Francisco Estuary (estuary) and the Sacramento–San Joaquin Delta (the Delta) in California face significant challenges in managing water resources during extended droughts. Zooplankton are a vital trophic link between phytoplankton producers and higher-level consumers such as predatory zooplankton and fish. However, there is still much to be learned about what drives zooplankton abundance and how they respond to drastic changes in environmental conditions, such as droughts. We found that during drought years zooplankton abundance and distribution changes varied for examined taxa. Significant declines in the abundance of Daphnia spp. and the copepod Pseudodiaptomus forbesi occurred in the Suisun Marsh and Suisun Bay regions. In contrast, abundance of the non-native copepod Limnoithona tetraspina increased in Suisun Marsh and the South-Central Delta during those same drought conditions. Salinity is a strong determinant of the presence and abundance of the studied taxa, and we showed that changes in the distribution of salinity as a result of low outflow conditions were an important factor in the regional abundance of zooplankton. Because of the expected increase in the frequency and severity of regional droughts, understanding how these conditions affect zooplankton in the estuary will benefit scientists and resource managers who aim to improve conditions for native fishes.

Zooplankton provide critical food for threatened and endangered fish species in the San Francisco Estuary (estuary). Reduced food supply has been implicated in the Pelagic Organism Decline of the early 2000s, and further changes in zooplankton abundance, seasonality, and distribution may continue to threaten declining fishes. While we have a wealth of monitoring data, we know little about the abundance trends of many estuary zooplankton species. To fill these gaps, we reviewed past research and then examined trends in seasonality and abundance from 1972 to the present of three key but understudied zooplankton species (Bosmina longirostris, Acanthocyclops spp., and Acartiella sinensis) that play important roles in the estuary food web. We fit Bayesian generalized additive mixed models of each taxon’s relationship with salinity, seasonality, year, and geography on an integrated database of zooplankton monitoring in the upper estuary. We found marked changes in the seasonality and overall abundance of each study species. Bosmina longirostris no longer peaks in abundance in the fall months, Acanthocyclops spp. precipitously declined in all months and lost its strong relationship with salinity, and A. sinensis adult abundance has become more strongly related to salinity while juveniles have developed wider seasonal abundance peaks. Through these analyses, we have documented the relationship of each species with salinity and seasonality since the beginning of monitoring or their introduction, thus increasing our understanding of their ecology and importance in the estuary. These results can inform food-web models, be paired with fish data to model the contributions of these species toward fish abundance trends and be mirrored to elucidate other species’ trends in future studies.

Wetland restoration is a key management tool for increasing food availability for at-risk fishes in the San Francisco Estuary. To characterize the benefits of restoration sites, it is critical to quantify the abundance and composition of fish food resources in and near the wetlands. Characterization of zooplankton communities is considered particularly important, but accurate analysis of zooplankton samples is time-consuming and expensive. The recently established Fish Restoration Program (FRP) Monitoring Team assessed whether data from existing long-term monitoring surveys could be used to characterize shallow-water zooplankton communities prior to restoration. During the springs of 2017-2019, FRP collected zooplankton samples near the mouth of tidal wetland sites, or immediately outside future restoration sites, and compared them to concurrent samples collected in deep water by existing long-term monitoring surveys. We found very few differences in community composition between shallow and deep samples, though a few taxa were more abundant in shallow water. Seasonal and inter-annual differences in composition and abundance showed that restoration sites provide varying food resources over time. There was significantly higher total abundance of zooplankton in deep versus shallow water, which may be due to differences in zooplankton production, migration, or fish predation. There may also be inconsistencies in towing speed and gear type driving this result, rather than true habitat differences. This study indicates that monitoring of wetland restoration sites must rely on multiple years of data collected on the site, rather than relying on adjacent open-water sampling, and should include monitoring of epiphytic and epibenthic invertebrates as well as zooplankton.