San Francisco Estuary and Watershed Science

Multi-year droughts are ever-present and transformational features of California’s Mediterranean climate and can fundamentally affect the water quality and the ecosystem responses of the San Francisco Estuary and the Sacramento–San Joaquin Delta. This study assessed data collected by long-term monitoring programs over the past 46 water years (1975–2021) to evaluate how water quality in the estuary changes during multi-year droughts. Data were aggregated by region (South-Central Delta, North Delta, confluence, Suisun Bay, and Suisun Marsh) and season, then differences between multi-year drought periods, multi-year wet periods, and neutral periods were compared using generalized linear models. We found that multi-year drought periods altered multiple physical and chemical parameters in the estuary, increasing water temperature, salinity, water clarity, and nutrient levels. This trend was consistent across regions and seasons, with few exceptions. Increases in these parameters during drought periods were likely caused by reduced Delta inflows that intensified in each successive dry year because of reduced precipitation and managed estuarine inflows and outflows. Drought periods did not substantially affect tidal velocities within the estuary, which remained mostly consistent across wet and drought periods. Trends in chlorophyll concentrations during drought periods were more nuanced with higher concentrations occurring in the South-Central Delta region and during the winter and spring. Together, these results characterized drought in the estuary as warm, clear, high in nutrients, with patchy phytoplankton blooms (as indexed by chlorophyll), all of which have implications for higher trophic levels. Considering that droughts are expected to increase in frequency and intensity in California with climate change, understanding the effects of multi-year droughts on the water quality conditions of the estuary can help inform water management decisions.

Cyanobacterial phytoplankton blooms are more prevalent in the freshwater Sacramento-San Joaquin Delta (Delta) since the late 1990s, including blooms driven by overgrowths of potentially toxigenic organisms of the genus Microcystis. Data from 2014 to 2021 were used to show how flow dynamics, water temperature, and water clarity drive occurrence of Microcystis. We used a Microcystis bloom in the central Delta from 2021 as a case study for how novel monitoring tools can track blooms in real-time and be used post hoc to evaluate the effects of management actions.

Microcystis was detected throughout the Delta in all but the highest-flow years, and bloom incidence and severity increased during drier years. In the South Delta, Franks Tract, lower San Joaquin River, and Old River regions, where blooms are most prevalent, higher water temperatures and clarities combined with lower exports from state and federal water projects were the best explanatory factors for the occurrence of Microcystis blooms. Nutrient concentrations were lower in summer than in winter, but only became limiting at high phytoplankton concentrations.

We used satellite data and in situ continuous monitoring of flow, phytoplankton communities, and water quality to track hydro-biogeochemical conditions during the 2021 case study Microcystis bloom in the Central Delta. We did not find evidence that changes to Delta outflow regulatory standards contributed to this bloom, but changes in flow caused by a salinity barrier placed in west False River may have exacerbated the bloom. The frequency and severity of droughts are expected to increase in the future as a result of climate change, and our study demonstrates how continued monitoring of cyanotoxins, water quality, and phytoplankton communities could help improve management of cyanobacterial blooms in the Delta and other estuaries.

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.

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.”