Abstract: Surface water bodies play a vital role in maintaining ecological balance and supporting socio-economic development, especially in arid and semi-arid regions such as Mongolia. These regions are particularly sensitive to climate change, and variations in surface water can have far-reaching implications for environmental security and human livelihoods. To better understand the spatiotemporal dynamics and driving mechanisms of water body changes in Mongolia, this study constructed a comprehensive and continuous dataset of surface water bodies spanning from 1990 to 2023, using Landsat satellite imagery. The reliability of the dataset was thoroughly validated, and subsequent analyses were conducted to reveal long-term trends and patterns in water body changes across different size categories. Temporally, the results indicate a pronounced decline in surface water bodies prior to 2009, followed by a gradual recovery trend in the years thereafter. Notably, small water bodies (1–10 km²) and micro water bodies (<1 km²) experienced the most dramatic changes, with frequent appearances and disappearances. These small-scale water bodies have historically received limited research attention, despite their ecological significance. In contrast, medium and large water bodies exhibited relatively stable transformations, often fluctuating between medium and large size classifications. Spatial analysis reveals that regions such as the Southeast Gobi Basin and the Hangai Mountains Valley Basin—located in desert and Gobi environments—demonstrate heightened sensitivity to climate variations. These areas experienced the most substantial changes in water body distribution. Climatic variables such as precipitation and evapotranspiration, represented by the Standardized Precipitation Index (SPI) and the Standardized Precipitation Evapotranspiration Index (SPEI), were found to be strongly correlated with the number and surface area of water bodies. These indices effectively capture the impact of Mongolia’s wet-dry-wet climate cycles on surface water availability. Moreover, land use and socio-economic indicators such as cultivated land area and livestock numbers showed similar fluctuation patterns to those of water bodies, especially micro-sized ones. This suggests a potential linkage between the loss of surface water and decreased pasture quality and rain-fed agricultural capacity. The findings highlight the ecological importance of small and micro water bodies, which deserve greater attention in future research and water resource management strategies aimed at promoting sustainable development in Mongolia’s fragile environment.