The water-sediment conditions in the reservoir area had changed significantly after the operation of the Three Gorges Reservoir, which has had a profound impact on the water ecology of the reservoir area. In this paper, the dynamic characteristics of the water flow and sedimentation in the reservoir area before and after the operation of the Three Gorges Reservoir were summarized, and the changes in the water-sedimentation conditions after water storage were analyzed. The water environmental response characteristics under this newly formed water-sediment conditions were evaluated in terms of changes in water quality parameters, nutrients, heavy metals, and toxic organic pollutants after the reservoir storage. The ecological response characteristics of aquatic biotas were also explored based on the community changes of phytoplankton, benthic fauna and other key biological communities before and after the reservoir storage. Finally, the outlook for future research on the water ecological environmental effects of the Three Gorges Reservoir was proposed. This paper can provide support for the water ecological environment protection of the Three Gorges Reservoir.