The phytoplankton lake community model PROTECH (Phytoplankton RespOnses To Environmental CHange) was applied to the eutrophic lake, Esthwaite Water (United Kingdom). It was validated against monitoring data from 2003 and simulated well the seasonal pattern of total chlorophyll, diatom chlorophyll and Cyanobacteria chlorophyll with respective R2-values calculated between observed and simulated of 0.68, 0.72 and 0.77 (all P<0.01). This simulation was then rerun through various combinations of factorized changes covering a range of half to double the flushing rate and from −1 to +4 °C changes in water temperature. Their effect on the phytoplankton was measured as annual, spring, summer and autumn means of the total and species chlorophyll concentrations. In addition, Cyanobacteria mean percentage abundance (%Cb) and maximum percentage abundance (Max %Cb) was recorded, as were the number of days that Cyanobacteria chlorophyll concentration exceed two World Health Organization (WHO) derived risk thresholds (10 and 50 mg m−3). The phytoplankton community was dominated in the year by three of the eight phytoplankton simulated. The vernal bloom of the diatom Asterionella showed little annual or seasonal response to the changing drivers but this was not the case for the two Cyanobacteria that also dominated, Anabaena and Aphanizomenon. These Cyanobacteria showed enhanced abundance, community dominance and increased duration above the highest WHO risk threshold with increasing water temperature and decreasing flushing rate: this effect was greatest in the summer period. However, the response was ultimately controlled by the availability of nutrients, particularly phosphorus and nitrogen, with occasional declines in the latter's concentration helping the dominance of these nitrogen-fixing phytoplankton.