Abstract: Surface water bodies play a vital role in maintaining the ecological balance and supporting socioeconomic development, particularly 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 livelihood. 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 from 1990 to 2023 using Landsat satellite imagery. Dataset reliability was thoroughly validated, and subsequent analysis were conducted to reveal long-term trends and patterns in water body changes across different size categories. Temporally, the results indicated a pronounced decline in surface water bodies prior to 2009, followed by a gradual recovery trend 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 micro water bodies have historically received limited research attention, despite their ecological significance. In contrast, medium and large water bodies exhibited relatively stable transformations. Spatial analysis revealed that regions located in desert and Gobi environments (such as the Southeast Gobi and Hangay Uul Valley basins), demonstrated 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 standardized precipitation evapotranspiration index (SPEI), were found to be strongly correlated with the number and area of water body. These indices effectively captured the impact of Mongolia’s wet–dry–wet climatic cycles on surface water availability. Moreover, land use and socioeconomic indicators such as annual arable land area and livestock number showed fluctuation patterns similar to those of water bodies, particularly micro water bodies. This suggests a potential link between surface water loss, decreased pasture quality, and rain-fed agricultural capacity. These 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.