Abstract: It is significant for maintaining ecological security to study the impacts of the Three Gorges Dam Project on the surrounding ecological environment. At present, massive studies have revealed the impacts from the construction and water impoundment of the Three Gorges Dam on meteorology, vegetation, land use, and the occurrence of disasters. However, the impacts of the project on surface water-an important part of the Earth’s water resources-are still unclear, especially in the upper reaches of the Yangtze River. Based on multi-source data and the Google Earth Engine platform, this study analyzes the changes in permanent surface water, vegetation, and meteorological factors in the Chongqing area before (1990—2002), during (2003—2012) and after (2013—2019) the water impoundment of Three Gorges Dam Project. The results show: ① Both surface water and vegetation in the study area showed an increasing trend during 1990—2019 with different growth patterns and notably response to the water impoundment. In contrast, the temperature and precipitation continuously fluctuated but did not significantly respond to the water impoundment process during that period. ② The area of the permanent surface water in the study area increased at an annual rate of 18.32 km² during the water impoundment but did not greatly change before and after the water impoundment. The newly added permanent surface water was mainly distributed along the Yangtze River and its tributaries, especially in the middle part of the Chongqing section of the Yangtze River. Besides, a minority of it was distributed in some lakes and reservoirs. For example, the area of the Changshou lake increased by more than 20% during the water impoundment. ③ The normalized difference vegetation index (NDVI) increased by 18.55% in a stepwise way before, during, and after the water impoundment, which is attributable to joint effects of the increase in surface water and the restoration projects of degraded ecosystem. This study indicates that the water impoundment of the Three Gorges Dam Project has notable impacts on the spatial-temporal dynamics of the water resources in the Chongqing area. Meanwhile, it reveals effective evidence that the water conservancy projects can change the coverage and water resource distribution on the ground surface. All these will provide scientific basis for water resource management in the Chongqing area and even the whole Yangtze River Basin.