Floating solar photovoltaics, or floatovoltaics (FPV), are a relatively new form of renewable energy, currently experiencing rapid growth in deployment. FPV decarbonises the energy supply while reducing land-use pressures, offers higher electricity generating efficiencies compared to ground-based systems and reduces water body evaporation. However, the effects on lake temperature and stratification of FPV both sheltering the water’s surface from the wind and limiting the solar radiation reaching the water column are unresolved, despite temperature and stratification being key drivers of the ecosystem response to FPV deployment. These unresolved impacts present a barrier to further deployment, with water body managers concerned of any deleterious effects. To overcome this knowledge gap, here the effects of FPV-induced changes in wind speed and solar radiation on lake thermal structure were modelled utilising the one-dimensional process-based MyLake model. To resolve the effect of FPV arrays of different sizes and designs, observed wind speed and solar radiation were scaled using a factorial approach from 0% to 100% in 1% intervals. The simulations returned a highly non-linear response, dependent on system design and coverage. The responses could be either positive or negative, and were often highly variable, although, most commonly, water temperatures reduce, stratification shortens and mixed depths shallow. Modifications to the thermal dynamics of the water body may subsequently drastically alter biogeochemical processes, with fundamental implications for ecosystem service provision and water treatment costs. The extreme nature of response for particular wind speed and solar radiation combinations results in impacts that could be comparable to, or more significant than, climate change. As such, depending on how they are used, FPV have the potential to mitigate some of the impacts of climate change on water bodies and could be a useful tool for water body managers in dealing with changes to water quality, or, conversely, they could induce deleterious impacts on standing water ecosystems. These simulations provide a starting point to inform the design of future systems that maximise ecosystem service and environmental co-benefits from this growing water body change of use.