Fish mortality and hypoxic events occur in many coastal and inland systems and may result from natural or anthropogenically mediated processes. The effects of consequent changes in water biogeochemistry have been investigated for communities of benthic invertebrates and pelagic metazoans. The responses of micro-plankton assemblages, however, have remained largely unstudied. The northern basin of King Harbor, a small embayment within Santa Monica Bay, CA, USA, suffered a massive fish kill in March 2011 as a consequence of acute hypoxia. Dissolved oxygen concentrations < 0.1 ml l−1 were measured in the northern basin of the harbor for several days following the mortality event, and a strong spatial gradient of oxygen was observed from the northern basin to waters outside the harbor. The microplankton community within King Harbor differed significantly from a diatom-dominated community present in neighboring Santa Monica Bay. The latter region appeared unaffected by physicochemical changes, induced by the fish kill, that were observed within the harbor. A trophic shift was observed throughout King Harbor from a photoautotrophic-dominated assemblage to one of heterotrophic forms, with relative abundances of bacterivorous ciliates increasing by more than 80 % in the most impacted part of the harbor. Significant changes in community structure were observed together with dramatically reduced photosynthetic yield of the remaining phytoplankton, indicating severe physiological stress during the extreme hypoxia.