Abstract: In spite of providing considerable economic benefits, the operation of the Three Gorges Reservoir causes many ecological and environmental problems, especially the sediment deposition caused by the impoundment of the reservoir. The sediment deposition of the reservoir has profound impacts on the ecological environment of its water-level-fluctuating-zone (WLFZ). For example, the sediment deposition can change the topography and geomorphology of the WLFZ and bring nutrients to the WLFZ, which is beneficial to the plant growth and ecological functions of the WLFZ in barren patches. In order to determine the factors influencing the sediment deposition in the WLFZ during the impoundment of the Three Gorges Reservoir, and to provide a scientific basis for the protection and management of the ecological environment of the WLFZ, we selected twelve typical WLFZ sites along the Three Gorges Reservoir and monitored the sediment deposition depth from August 2017 to June 2018. The environment characteristics of each site were investigated. The results showed that: (1) During the impoundment of the Three Gorges Reservoir, the thickness of deposited sediments on the WLFZ of the Three Gorges Reservoir was determined by a set of environmental factors, such as the water course distance from the dam, elevation, riparian morphology, slope, and vegetation coverage of the WLFZ. (2) Among these environmental factors, the geological position of the WLFZ to the dam was the most important factor, the rest were elevation, vegetation coverage, and riparian morphology according to the degrees of their importance, and the slope has the weakest influence on the sediment deposition depths of the WLFZ.