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Artificial and natural water bodies, such as reservoirs, ponds, rivers and lakes, are important components of water-related ecosystems; they are also important indicators of the impact of human activities and climate change on surface water resources. However, due to the global and regional lack of artificial and natural water bodies data sets, understanding of the changes in water-related ecosystems under the dual impact of human activities and climate change is limited and scientific and effective protection and restoration actions are restricted. In this paper, artificial and natural water bodies data sets for China are developed for the years 2000, 2005, 2010, 2015 and 2020 based on satellite remote sensing surface water and artificial water body location sample data sets. The characteristics and causes of the temporal and spatial distributions of the artificial and natural water bodies are also analyzed. The results revealed that the area of artificial and natural water bodies in China shows an overall increasing trend, with obvious differences in spatial distribution during the last 20 years, and that the fluctuation range of artificial water bodies is smaller than that of natural water bodies. This research is critical for understanding the composition and long-term changes in China’s surface water system and for supporting and formulating scientific and rational strategies for water-related ecosystem protection and restoration.