Establishing floating photovoltaic (FPV) systems on aquaculture ponds can reduce demand for land use and affects food and solar energy production. This study investigated the water quality of aquaculture ponds with and without simulated FPV systems (40% surface area shading) at three sites: Chupei, Lukang and Cigu. Results indicated the FPV‐covered ponds exhibited lower mean values in biochemical oxygen demand and plankton biomass but higher oxidation–reduction potential relative to the control ponds. The FPV‐covered ponds exhibited lower pH, water temperature and level of dissolved oxygen relative to the control ponds in Chupei and Lukang. The results suggested that the FPV shading effect potentially reduced phytoplankton growth. All FPV‐covered ponds exhibited 1.1, 1.2 and 1.4 times greater yields in giant freshwater prawn, tilapia and milkfish without any effect on the growth of cultured species. These results demonstrate the potential benefits and defects of combining aquaculture with FPV systems.