San Francisco Bay, California, typically has chlorophyll a (chl-a) concentrations below 10 µg L⁻¹, despite nutrient loadings exceeding those in many estuaries with recurring harmful algal blooms (HABs). However, in August 2022 there was a Heterosigma akashiwo (raphidophyte) bloom with chl-a concentrations exceeding 450 µg L⁻¹, resulting in widespread hypoxia and fish die-off. We used protist community (18S ribosomal ribonucleic acid gene metabarcoding) and environmental data collected 2–3 times per month from 2015–2023 to assess differences between 2022 and other years, and capture dynamics pre-, during, and post-bloom. The 2022 protist community clustered separately from other years in non-metric multidimensional scaling and hierarchical cluster analyses. A diatom bloom in June generated the highest median June chl-a concentration (15 µg L⁻¹) recorded between 1977–2023 and drew down nutrients (nitrogen, silicate), leading to the establishment of a heterotrophic community in July with low dinoflagellate abundance (0.9% of protists versus 5.9% average in other years). The absence of dinoflagellates, potentially including H. akashiwo predators, plus suitable habitat (13–14 daylight hours, temperatures 17–21˚C, nitrate concentrations 17–24 µmol L⁻¹, neap tides) likely provided opportunity for H. akashiwo to proliferate from 0.03% to 48% of protists between July 20 and August 25. As the bloom collapsed, the genus Gyrodinium (dinoflagellate predator of H. akashiwo) increased from 3.0% to 52% of protists between August 25 and August 31, likely exerting grazing pressure. Results show that antecedent protist community dynamics play important roles in shaping HABs, and interactions between biotic and abiotic factors govern the development of blooms.