China is home to 97,246 reservoirs, most of which are sub-deep water reservoirs characterized by seasonal stratification and multiple interfaces in the water body. The prominent eco-environmental problems, such as eutrophication and accidental deterioration in water quality, restrict reservoir construction. Compared to natural lakes, reservoirs have specific geologic backgrounds and eco-environmental characteristics, which manifest in the following aspects: (a) the origin of the water environment and ecological system of the reservoir is different from natural lakes; (b) sediment is rich in organic matter and nutrients; (c) water eutrophication and heavy metal pollution are tightly interlocked; (d) multi-interface and seasonal stratification control the key physicochemical and biological processes; (e) the cumulative effect of the material cycle has an important influence on the water environment and ecological security; (f) artificial regulation of water level leads to the ecological degradation of the hydro-fluctuation belt; and (g) the slow response of the aquatic ecosystem to the reduction of external load. Research on the eco-environment of sub-deep water reservoirs trails that of natural lakes in China. After describing the eco-environmental characteristics of reservoirs in China, we address potential challenges and propose future research directions to develop a full understanding of the complex biogeochemical processes prevalent in reservoirs.