Nutrient delivery in subtropical coastal systems is predominantly via acute episodic high flow events. However, continuous nutrient discharges from point sources alter these natural fluctuations in nutrient delivery, and are therefore likely to lead to different ecosystem responses. The aim of this study was to assess how a reduction in chronic sewage nutrient inputs affected chlorophyll a (chl a) concentrations in a subtropical bay, in the context of seasonal fluctuations in riverine nutrient inflows. Reduced nutrient inputs from a large sewage treatment plant (STP) resulted in lower mean dissolved inorganic nitrogen and phytoplankton chl a concentrations during both the austral summer wet and winter dry season. This was measurable within 10 y of nutrient reductions and despite the confounding effects of nutrient inflow events. Our study demonstrates that reductions in STP inputs can have significant effects on phytoplankton biomass despite confounding factors over relatively short time frames.