Prospect Reservoir, a Greater Sydney water supply reservoir, has historically been characterised as oligotrophic, with clear water conditions and an established macrophyte bed. It has experienced dynamic changes to its hydrological regime linked to supply operations with water transfers from multiple sources including Warragamba Dam, used to ensure supply system resilience. In this study, 10 years of monitoring data was used to evaluate long-term changes in the reservoir’s phytoplankton community and its relationship to environmental parameters and operational activity. Results showed that prolonged drawdown and subsequent refill, coincided with a significant increase in phytoplankton biovolume, with episodically high biovolume of dinoflagellates (Ceratium and Peridinium) during the Summer/Autumn period. Post-bushfire inflows resulted in the greatest change to the phytoplankton community. The use of functional group classification and PCA highlighted the shift from a dominance of groups that tolerate nutrient poor conditions to an increase in meso-eutrophic groups. RDA revealed that this community change corresponded with increase in some nutrients and trace metals, reduced Secchi depth, and higher chlorophyll-a. Results suggest the Reservoir has shifted from an oligotrophic system towards mesotrophic following the bushfires. Furthermore, operational activities including prolonged drawdown events, and inflow regularity and quality, have an effect on the phytoplankton community.