Sydney Harbour is a highly diverse but impacted estuary. Infrequent, heavy precipitation events result in stormwater inflows into the estuary causing large nutrient fluxes. The influence of such nutrient enrichment on the phytoplankton community, which are important contributors to ecosystem function, have not been explored. Therefore, this study aimed to evaluate the changes in phytoplankton assemblages associated with heavy rainfall events. Unraveling such changes in phytoplankton composition in response to environmental perturbations is key to predicting the future health of this important estuary.