Freshwater flow events drive phytoplankton productivity in subtropical coastal river systems. However, few studies have the necessary temporal and spatial resolution to fully characterise the effect of events on the distribution of phytoplankton across the full river-estuary-bay continuum. The present study characterised the response of phytoplankton to high-flow events in an Australian subtropical system; and identified the primary drivers of this response. During high-flow events, the concentration of phytoplankton chlorophyll a (Chl a) initially declined in the estuary, a response primarily driven by the shortened water-residence time. In the bay, phytoplankton growth in the near-shore zone was light limited; however, nutrients stimulated phytoplankton growth on the seaward edge of the river plume. During the post-high-flow phase, the concentration of Chl a in the freshwater reaches peaked downstream, where catchment-derived nutrients accumulated. In the estuary, elevated nutrient loads stimulated phytoplankton growth upstream and downstream of the light-limited zone. In the bay, nitrogen availability declined, and Chl a declined with an increasing distance offshore. The phytoplankton response to events documented in the present study can be used to identify when and where phytoplankton in subtropical systems may be strongly influenced by changes in the magnitude of nutrient, sediment and freshwater loads associated with high-flow events which result from anthropogenic pressures within the catchment. Journal compilation © CSIRO 2013.