Abstract: Under the influences of climate change and human activities, the temporal and spatial variations of surface water bodies in Mongolia directly impact the country's agricultural and pastoral development, as well as the ecological security of northern China. To explore the temporal and spatial patterns of water body changes in Mongolia, this study, based on the GEE platform and Landsat remote sensing data, extracted and established a dataset of surface water bodies in Mongolia from 1990 to 2023. After validating the reliability of the new dataset, the study analyzed the trends and causes of changes in various water bodies over the past 30 years. The results indicate that, in terms of the time series, water body changes exhibited a trend of initial decline followed by an increase. By the end of the study period, the number of water bodies had decreased by 69, 200, and the total area had shrunk by 367.6 km². Significant differences were observed in the changes among water bodies of different sizes, with small water bodies (1–10 km²) and micro water bodies (<1 km²), which historically received less attention, experiencing the most dramatic changes. Medium and large water bodies mostly underwent transformations between different types of water bodies. Spatially, areas such as the Southeast Gobi Basin and the Hangay Uul Basin, bordering China, exhibited more intense water body changes and were more sensitive to environmental changes. The causality analysis revealed that climate factors, particularly rainfall and the Standardized Precipitation Index (SPI), had a significant impact on changes in the number and area of water bodies. Furthermore, a positive feedback relationship was found between water body changes and cultivated land area and livestock scale. This is closely related to Mongolia’s dependence on small and micro water sources for its nomadic pastoralism.