In this study we evaluate several eco-environmental vulnerabilities caused by water level fluctuations of the Three Gorges Reservoir. The Three Gorges Dam (TGD) has been inserted in the middle of a biodiversity hot spot in south-central China. The fluctuation zones of the Three Gorges Dam are made up of very fragile ecosystems which will require careful management in order to preserve them as a unique and rich source of information. Behind the dam water level fluctuate between 145m and 175m, resulting in a belt of water which changes in depth and length throughout the year. In the winters of 2008 and 2009 the pool topped behind the Three Gorges Dam at 175 m above sea level. The result of the increased pool was upstream flooding extending to within reach of the city of Chongqing. These water levels flood former cities, homes, and farm fields of about 1.5 million people seasonally for up to 7 months of the year. So the studied area has many eco-environmental problems, such as landslide, water erosion, pollution, and landscape destruction and so on. And in this study we used landslide, water erosion, pollution, and landscape deterioration as indicators of vulnerability to flooding. Vulnerability varies widely across communities, sectors and regions. It has no universally accepted definition. This diversity of the “real world” is the starting place for a vulnerability assessment. And it is essential for users to define vulnerability in their own context. In this paper, we defined the concept of “vulnerability” as an inherent property of a system arising from its internal characteristics which make it more or less susceptible to external hazards. Each of our indicators of vulnerability used a set of unique measures. The individual measures of each indicator were ranked between 1 and 5. The geometric mean of these ranks was used to create a final index of vulnerability for each indicator. Using ArcGIS the vulnerability indices were assigned to a grid corresponding to the fluctuation belt. We conducted an overlay analysis of the grids to determine the location and number of eco-environmental problems along the fluctuation belt. The vulnerability indices for landslide, water erosion, pollution, and landscape destruction had high vulnerability ranks only 18 to 35% of the time. However, we found that these high ranking vulnerability problems did not overlap across the fluctuation belt. As a result 70% of our study area had at least one high ranking eco-environmental problem and 30% of the area had two or more. Therefore, every part of the Three Gorges Reservoir Area is experiencing at least one eco-environmental problem. Many countermeasures for the water-level-fluctuation area have already been proposed including: planning rationally, establishing slope protection, and adjusting rural industrial structures along the two sides of the area. The results from this study provide a scientific base for the government to make policies for distributing relief funds and help the regions to improve their capabilities of adaptability and mitigation. However, in order to take advantage of this opportunity, international funding and long-term collaborations will be needed.