The Three Gorges Project is a key pivotal hydro-project in the Yangtze River Basin for the protection and security of water resources, which has been attracting worldwide attention over the past decades. Since the impoundment of the Three Gorges Reservoir in 2003, the project has created great economic, social, and ecological benefits in terms of flood control, hydropower generation, navigation, and water supply. Meanwhile, the reservoir formation has drastically transformed the 600km natural river reach of Yangtze, from Chongqing to Yichang, to a large river-valley dammed reservoir with deep water regulated by the dam. Such has created unique landscapes and habitats within the reservoir, e.g., drawdown area along the shorelines, reciprocal fluctuating backwater water area between tributaries and the main stem, etc. In addition, the regulation of the reservoir discharge also leads to new patterns of spatiotemporal variations of hydrological and biogeochemical parameters, e.g., sediment transport, fluvial equilibrium of downstream channels, nutrient exports, etc. The river-lake relationships in the mid and lower reach of the Yangtze have been becoming more complex than before 2003. The Yangtze River basin is now in a post-Three-Gorges-Project era. To summarize the state of research on the ecological and environmental effects caused by the Three Gorges Reservoir in the past 20 years, the editorial board of the Journal of Lake Sciences invited us to organize this special issue. The call for papers was announced in April 2022. Since then, more than 60 manuscripts have been received, and after extensive reviews, 25 of them were finally accepted for publication. The manuscripts collected in the special issue are informative and relevant, representing the knowledge-of-the-art of the ecological and environmental effects of the giant hydro-project in history. (1) In the area of hydrology and water resources, sediment transport in the mid and lower reaches of the Yangtze, as well as their exchange with the Dongting Lake and Poyang Lake, were elaborated. The special issue also collected novel methodologies for the flood prediction of the reservoir inflow, in particular, the fluctuation of a downstream riverbed after the operation of the Three Gorges Reservoir, as well as the situation of river scouring and channel depth variation, were extensively discussed. (2) In the area of water environment and aquatic ecology, the special issue systematically addressed the ecological and environmental effects caused by hydrological and hydrodynamic conditions. The important biogeochemical cycles of nitrogen within the soil-plant-microbial interactions in the reservoir drawdown area were also reviewed and discussed profoundly. It highlighted the tributaries of the Yangtze in the reservoir, exhibiting the trends of eutrophication, had potential risks of algal blooms. However, the causal chain of phytoplankton growth in the main stem and tributaries should also be taken into further attention. (3) In the area of watershed biodiversity conservation, the special issue collected manuscripts on the evolution of vegetation communities and adaptive strategies of dominant populations in the drawdown area. The evolution of vegetation productivity in the wetland of Poyang Lake was discussed. The research on drifting egg-producing fish populations was also included in the special issue. (4). In the watershed water security, manuscripts in the special issue discussed the air-water heat transfer process and thermal stability of the water column in the reservoir. Rather than regionally, we were delighted to find that modeling analysis revealed that the potential climatic effect caused by the project were mainly limited to the local scale or near-surface layer. Undoubtedly, this result seemed to be positive with considerable significance. (5) As China’s largest reservoir, greenhouse emissions from the reservoir have been the concern of academic communities, stakeholders, and policymakers, particularly about its potential contribution to China’s road to carbon neutrality. The special issue collected recent advances and outlooks on field monitoring and analysis of CO2 and CH4 fluxes in the reservoir. We believed that this would be a research hot spot shortly. This is the fourth special issue in the Journal of Lake Sciences over the past decade. It is not the number of manuscripts that counts but the quality of the research. In the future, we will continue to focus on the Three Gorges Reservoir, and report on the state of the research on hydrology, ecology, and environment and watershed water security in the Yangtze River Basin in the Post-Three-Gorges-Project era. These efforts will better serve the Great Protection Strategy of the Yangtze River and ecological civilization in China.