A decade of observation in South San Francisco Bay demonstrates that estuarine phytoplankton biomass fluctuates at the time scale of days to weeks, and that much of this variability is associated with fluctuations in tidal energy. During the spring seasons of every year from 1980–1990, episodic blooms occurred in which phytoplankton biomass rose from a baseline of 2–4 mg chlorophyll a m–3, peaked at 20–40 mg chlorophyll a m–3, and then returned to baseline values, all within several weeks. Each episode of biomass increase occurred during neap tides, and each bloom decline coincided with spring tides. This suggests that daily variations in the rate of vertical mixing by tidal stirring might control phytoplankton bloom dynamics in some estuaries. Simulation experiments with a numerical model of phytoplankton population dynamics support this hypothesis. The model incorporates biological processes (light-dependent growth, zooplankton grazing, benthic grazing) and physical processes (sinking, vertical mixing) as controls on the biomass distribution of phytoplankton in a 10-m water column. Numerical simulations indicate that phytoplankton dynamics are highly sensitive to the rate of vertical mixing (parameterized as an eddy diffusivity Kz), such that biomass increases rapidly at small Kz (5 m2 d–1), but not at large Kz (50 m2 d–1). Cyclic variation of Kz between 5 and 50 over a 14-d period (simulated neap-spring cycle) yields simulation results that are similar to bloom events observed in this estuary.