A harmful algal bloom of Heterosigma akashiwo in the Sundays Estuary, South Africa, changed the bacterial community structures. Flavobacteria increased during the bloom, indicating their role in breaking down algal matter. Halieaceae were common during the bloom, while other bacteria like Synechococcales and Cryomorphaceae were linked to the decay of the bloom. Rhodobacteraceae, mainly Litorimicrobium, were also associated with the bloom. The bacterial community profiles were influenced by the bloom-forming species and the lack of research on estuarine harmful algal blooms.