Since the impoundment in 2003, the water environment and algal bloom in the tributaries of the Three Gorges Reservoir (TGR) have become widespread concerns. This paper reviews the research on its water environment in the past 20 years, systematically summarizes the hydrodynamic characteristics between the mainstream and tributaries and their eco-environmental impacts, and looks forward to the new perspective, new content, and new methods in TGR. The conclusions include: (1) After the impoundment of the TGR, the mainstream and tributaries are differentiated hydrodynamics. The water body in the mainstream gradually change from 'River-type’ (residence time < 20 days) in the upstream into 'Transitional-type’ (residence time >300 days) in the front of dam, but water body in the tributaries are 'Lake-type’; (2) The hydrodynamics phenomena, e.g., density current driven by the density (water temperature) difference between mainstream and tributary, flow oscillation driven by daily regulation and meteorologically-driven near-surface mixing, are prominent and ubiquitous in tributaries of TGR, and dominate the thermal stratification and mixing process in the tributary bay; (3) The unique hydrodynamic process in TGR have profound impacts on the thermal stratification, nutrient transport, water bloom, and greenhouse gas emissions. The ecological scheduling to improve the hydrodynamic process and water environment has become an important technical means. How to synthesize the above findings into a new system theory or method in Three Gorges Reservoir, which can be applied to the large-scale and deep-reservoir ecological environment research and serve joint multi-objective optimization scheduling practice in cascade reservoirs, is still the future efforts. By summarizing the hydrodynamic of TGR and its eco-environmental effects, this study helps to deepen the understanding of the hydrodynamic processes of large river-type reservoirs.