The water bodies existing along highways in the high altitude areas of the Qinghai–Tibet Plateau (QTP) will aggravate subgrade settlement and road damage, and affect the long-term stability of road networks. Based on remote sensing and geographic information system (GIS) techniques, this study analyzed the changes in the number and area of water bodies along the G109 and G219 highways in the QTP in the past 20 years. The results showed that between 2000 and 2019, the number of water bodies along the two highways increased by 24 and 19%, respectively, and their area increased by 26 and 19%, respectively. The area and the number of water bodies >1 km2 in the permafrost area and those <1 km2 in the seasonal permafrost area both changed significantly. The change in the number of water bodies in the permafrost area was positively correlated with annual average temperature, while that in the seasonal permafrost area was significantly positively correlated with annual precipitation. This study provided basic data that could be used in studies on the interrelationship between engineering and water bodies within the context of climate change and will contribute to revealing the mechanisms through which engineering projects affect frozen soils.