Photovoltaic energy is projected to represent the largest share of global energy supply by 2050. Floating photovoltaic systems (FPVs) are expected to expand rapidly but their impacts on aquatic ecosystems remain poorly understood. Yet, there is potential for design choices, including the potential for “light island” designs (removing panels across the array to allow for increased light penetration in the water column), to mitigate potential negative effects. Here, we use three-dimensional computational modelling (Delft3D-FLOW), to investigate how the thermal response of a water body is likely to change with multiple light islands designs. The model predicted that the FPVs’ effects on the water column temperature vary seasonally and by depth for all designs: wind sheltering effects prevail over shading during warmer months, leading to stronger thermal stratification compared to the simulation without FPVs. Surface coverage variation was the main driver of thermal responses, even for small changes in surface coverage (∼5%); light island designs had a limited impact on water temperature and thermal stratification. However, light islands may also impact primary production through enhancement of underwater light availability. Further examination of the effects of light islands on water body biological and chemical responses is required as part of efforts to ensure that FPV deployment strategies balance energy production and sustainable water management.