To date, most studies focus on the ecological and environmental effects of land-based photovoltaic (PV) power plants, while there is a dearth of studies examining the impacts of water-based PV power plants. The effects of a fishery complementary PV power plant, a kind of water-based PV technology, on the near-surface meteorology and aquaculture water environment were investigated in coastal aquaculture ponds in southeast China. The results showed that PV prevented 89~93% of the solar radiation on the surface of the pond, resulting in an average reduction in water temperature of 1.5 °C and a substantial decrease in light intensity of 94%. Furthermore, it weakened the wind speed by 41~50% and elevated the surface air temperature by an average of 0.6 °C. In addition, PV power results in an impressive decrease in chlorophyll-α of 72~94% and a notable increase in dissolved oxygen (DO) concentrations of 8~24%. PV power also reduced the concentration of labile phosphate, active silicate, total nitrogen, total phosphorus, and total organic carbon. However, the PV power did not have a substantial influence on the concentrations of nitrate and ammonium. Our results highlight that fishery complementary PV power plants may be able to improve water quality and benefit shade-loving species.