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 rib...