With the aggravation of global warming and the increasing demand for energy, the development of renewable energy is imminent. Floating photovoltaic (FPV) is a new form of renewable energy generation. However, the impact of FPV on the aquatic environment is still unclear. By long-term empirical monitoring and data analysis, this paper reveals the shading effect of large-scale FPV power station on aquatic environment for the first time. The results show that: (1) Compared with the non-photovoltaic (NP) zone, FPV only significantly reduces the concentration of dissolved oxygen in the photovoltaic (P) zone. (2) The concentration of chlorophyll a, nitrate nitrogen and total phosphorus increase, while pH and ammonia nitrogen decrease. FPV only causes an effect of the same order of magnitude as the initial concentration, and has no significant adverse effects on the nutritional status of the water body at a coverage ratio less than 50%. (3) FPV has a cooling effect on the water body during the daytime and a thermal insulation effect at night, with the most pronounced impact on peak water temperature (Tw). The heating and cooling process of Tw in P zone usually lags behind the NP zone by 1–3 h. The diurnal fluctuation and vertical difference of Tw as well as the stability of water body are reduced under the shading of FPV, alleviating the influence of climate change on Tw and water body stratification. (4) If 10% of the water area larger than 1 km2 in China are used to develop FPV, more than 900 million tons of CO2 emissions can be reduced, and about 5 billion m3 water can be saved, which is significant in the context of climate change. In general, this paper provides a reference for the future aquatic environmental impact assessment of FPV and the formulation of related policies.