Drought and Aquatic Vegetation Alter Water Clarity and Fish Assemblages in Freshwater Tidal Ecosystems of the Sacramento-San Joaquin River Delta

Abstract Tidal freshwater habitats in the Sacramento-San Joaquin River Delta (Delta), USA, face multiple environmental stressors, including declining turbidity and invasion by submersed aquatic vegetation (SAV). We used a decade of monitoring data (2013–2023) in two tidal slough networks in the north Delta to (1) estimate trends in SAV, water clarity (Secchi depth), and abundance of pelagic, littoral, and benthic fish species; (2) identify the role of droughts and SAV expansion on water clarity dynamics; and (3) quantify relationships between changing habitat conditions and fish assemblages. Two multi-year droughts, concurrent with rapid expansion of invasive SAV, triggered a regime shift from turbid to clear conditions in tidal freshwater sloughs, with average Secchi depth increasing from 35 to 150 cm by 2020. Secchi depth decreased with local precipitation (e.g., sediment loading) and increased with SAV. Abundance of non-native littoral fishes increased with higher SAV (bluegill— p = 0.003; redear sunfish— p = 0.0001, largemouth bass— p = 0.0002). SAV was negatively associated with abundance of non-native pelagic and benthic species (striped bass— p = 0.03, threadfin shad— p = 0.002, white catfish— p = 0.004) and with a native littoral species (tule perch— p = 0.015), whereas relationships between water clarity and fish abundances were more complex. Abundances of some native fishes (hitch, tule perch, prickly sculpin) increased following a sudden decline in SAV (2021–2022) combined with a decline in water clarity during a record wet year (2023). Dynamic responses of fish assemblages to SAV and water clarity in the north Delta demonstrate the importance of hydroclimatic variation in mediating the effects of invasive SAV on tidal freshwater ecosystems.