This paper introduces the water environmental and aquatic ecological status of the Three Gorges Project. The impacts of the project on the aquatic environment, involving hydrological regimes, water quality, reservoir eutrophication, and water blooms in the tributaries, are analyzed. The project’s impacts on aquatic ecology, including the aquatic ecosystem, food organisms, fish species, and rare aquatic animals, are also analyzed. Several measures are proposed to protect the water environment, including optimization of reservoir regulation, urban sewage treatment, industrial waste water control, rural non-point source pollution control, and drinking water source protection. For the protection of the aquatic ecosystem, some measures are put forward, including habitat conservation, species conservation, artificial enhancement and release of fish, and ecological reservoir regulation.