Assessing the status and drivers of phytoplankton blooms along the riverine to freshwater-tidal continuum in a modified delta

Shifts in phytoplankton communities, from beneficial taxa that fuel food webs to harmful taxa that degrade water quality, are often linked to anthropogenic modifications to estuaries. We analyzed monitoring data from 2000 to 2023 in the heavily modified southern, landward portion of the Sacramento-San Joaquin Delta (California, USA) to determine the status and drivers of phytoplankton abundance and community composition along the riverine to freshwater tidal transition. Diatoms and green algae dominated the phytoplankton community, especially when chlorophyll a (chl-a) concentrations exceeded 16 µg L^− 1. Common riverine diatoms (e.g., Cyclotella and Aulacoseira) dominated upstream riverine stations, while taxa associated with tidally influenced conditions (e.g., colonial cyanobacteria, cryptophytes) were more prevalent in western, freshwater tidal stations. The potentially toxigenic cyanobacterium, Microcystis, was present each summer, but was not associated with elevated chl-a or cyanotoxins (microcystins were detected in 12% of samples with a maximum concentration of 3.9 µg L^− 1). A Bayesian ordinal regression showed that mean prior week water speeds below 0.18 m s^− 1 and water temperatures above 22 ˚C were associated with the presence of Microcystis. Random forest modeling to assess factors associated with phytoplankton blooms (chl-a > 16 µg L^− 1) found that mean prior week turbidity, inflows from the San Joaquin River, region, and mean prior week water temperature were important drivers of blooms. These modeling results emphasize the importance of hydrodynamics in controlling phytoplankton dynamics in lowland rivers and tidal deltas, offering insights for how anthropogenic impacts on flow regimes may affect the base of estuarine food webs.