The implementation of water-surface photovoltaic systems as a source of renewable power has expanded rapidly worldwide in recent decades. Water-surface photovoltaic avoids negative impacts on terrestrial ecosystems, while the impacts on aquatic physical and chemical properties and biodiversity are unclear. To understand the ecological and environmental impacts of water-surface photovoltaic systems, here we conducted a field survey on water physical and chemical properties, plankton and bird communities of 26 water-surface photovoltaic systems in the Yangtze River basin in China during the winter and summer of 2022. We found that water-surface photovoltaic systems decreased water temperature, dissolved oxygen saturation and uncovered area of the water surface, which caused a reduction in plankton species and individual density, altering the community composition. Water-surface photovoltaic systems also caused an overall decrease in bird diversity and changed bird community compositions. These findings suggested that water-surface photovoltaic systems have impacts on the water environment and ecology. Since water-surface photovoltaic systems will continue to expand in the future, our results emphasize that rational planning is critical for the sustainable development of water-surface photovoltaic systems and the protection of the aquatic environment and biodiversity.