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Open Access Publications from the University of California

The Anatomy of a Drought in the Upper San Francisco Estuary: Water Quality and Lower-Trophic Responses to Multi-Year Droughts Over a Long-Term Record (1975-2021)


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.

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