Water is a basic resource for the development and production of human society. With the continuous development of remote sensing technology and cloud computing technology, the Google Earth Engine (GEE) platform has become an important means for large-scale and long-term surface water bodies analysis and mapping. Using Landsat 5 TM and Landsat 8 OLI satellite data, the spatial-temporal variation characteristics of surface water bodies in Mongolia from June to September 1985—2023 are analyzed. The results show that the area of surface water bodies in Mongolia showed a downward trend from 1985 to 2023, and the area of stable water bodies decreased from 15547.71 km² to 14452.13 km². Among them, large water bodies remained relatively stable, and small lakes and rivers changed mainly. The analysis results of this paper provide an important basis for an in-depth understanding of the ecological and environmental changes in Mongolia, and provide a direction for accurately predicting the future water resources and environmental changes in Mongolia and the effective management and protection of water resources.