Floating solar photovoltaics (FPV) are an emerging form of solar energy installation, with systems deployed on water bodies worldwide. The rate of deployment has increased in recent years as the drive to decarbonise the energy mix intensifies. FPVs could interact favourably or detrimentally with the provision of freshwater ecosystem services with implications for the United Nations Sustainable Development Goals. Yet, potential co-benefits and threats are poorly resolved, posing a barrier to future deployments and a potential threat to freshwater ecosystem services on which society relies. There is scope to use FPVs as a means to manage water quality, in addition to providing low carbon electricity. To enable the response of individual water bodies to be assessed quantitatively, we simulated the effects of FPVs on water body process and function using a case study water body within the UK. We found water body response to a FPV was contingent on siting location on the water body, with modifications to lake thermal properties and algae proliferation moderated by this deployment decision. For example, with 40 % FPV array coverage, algal biomass was reduced by up to 81 % when the array was deployed on a faster-flowing area of the reservoir compared to the reservoir with no FPV coverage. In contrast, algal biomass was only reduced by up to 50 %, compared to no FPV coverage, if the same array was deployed on a slower-flowing area. Overall, we found the decline in algal biomass usually offset any undesirable changes to species composition. Cooler water temperatures, reduced stratification duration and a worsened light climate in the presence of FPV switched species composition to diatoms and green algae, reducing the dominance of harmful blue-green algae, which pose a significant threat to water quality. Consequently, FPV could help control harmful algal blooms on some water bodies, but the scale of impact could be moderated by siting location on the water body. Our findings highlight the importance of making informed deployment decisions and the pertinence of improving understanding to ensure future FPV installations minimise detrimental impacts and maximise opportunities for water quality improvements.