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.

Aquatic invasive species have drastically changed how the San Francisco Estuary functions. During the past 2 decades, the effects of invasive species in the estuary may have increased in response to frequent and severe drought conditions. The invasive overbite clam (Potamocorbula amurensis), and the Asian clam (Corbicula fluminea) have well documented consequences on the estuarine food web, but their responses to drought are not well understood. Another invasive species, the jellyfish Maeotias marginata, can further affect the food web, but these effects have not been studied. We investigated the population responses of these invasive species to dry years and their potential effects on the pelagic food web using data from the Interagency Ecological Program’s monitoring surveys. We found M. marginata rapidly moves upstream with changing salinities during dry years, though it sees its highest abundance during high-outflow years in Suisun Bay and Suisun Marsh. Grazing rates of M. marginata in the estuary have not been quantified but are potentially high during localized blooms. The two invasive clams overlap in distribution, but have opposite population responses to drought conditions, with increases in P. amurensis densities and decreases in C. fluminea densities in dry years. With increasing P. amurensis densities, the clams’ combined annual filtration rates increase during drier years in the confluence and Suisun Marsh. Like M. marginata, P. amurensis also shifts upstream during droughts, but because adults cannot move immediately with a change in salinity, the population center of distribution shifts upstream the year after a dry year as a result of juvenile recruitment. If multiple dry years occur in a row, and both P. amurensis and M. marginata move upstream together, their effects on the food web could be compounded, and phytoplankton and zooplankton biomass could steeply decline in the confluence, affecting higher trophic levels in the estuary.

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.

Droughts have major effects on estuaries because freshwater entry is one of the defining features of an estuary, and freshwater flow is an important variable that determines the interannual change in the environment. In the upper San Francisco Estuary (the Sacramento–San Joaquin Delta, Suisun Bay, and Suisun Marsh), the Mediterranean climate includes frequent multi-year droughts. To assess ecosystem responses to droughts in the upper estuary, the Interagency Ecological Program Drought Synthesis Team assembled a set of flow, water quality, chlorophyll, zooplankton, and fish data from 1975 to 2021 to test for differences between multi-year droughts and multi-year wet periods and tested for linear relationships between each variable and the Sacramento Valley Hydrologic Index (see definitions and relationships as outlined in Appendix A). Our models showed droughts decreased Delta outflow, project exports, zooplankton in Suisun Bay, and some fish species. We also found that droughts increased water clarity, salinity, nutrients, chlorophyll in the South Delta, zooplankton in the South Delta, and water residence time. Although our analyses only tested correlations, we hypothesized that most of the food-web responses could be traced to increased residence time, decreased transport rates, or both. However, some responses may have been caused by secondary effects, including shifts in salinity gradients, regional changes in water quality, or differences in top-down effects of increased predation and grazing rates. With increased frequency of droughts in the future, this increasingly low-outflow, warming, clearing estuary—which is invaded by non-native species and has low pelagic fish production—is rapidly becoming the new “normal.”