In the past about two decades, mega-reservoirs impounded in the upper basins have profoundly altered the runoff and its regimes in the lowland reaches of the Yangtze River. Annual, autumn (Sept.-Nov.) and October flow discharge via the Yichang gauge station downstream of the Three Gorges project (TGP) have decreased by 11%, 29.6% and 40%, respectively, with remarkable higher coefficient of variation. The rare scenery of dry-year in frequency 97% has become 80%-85% comparing with their previous counterparts before 1990. On the other hand, sediment load downstream Yichang reduced by 93%, while by 70% across the Datong gauging station to the estuary. As a result of clear-water flow, scouring and incision in the mid-and lower reaches exceeded 2.1 km³ in total and 1-3 m in main channel elevations, surpassed the maxim limit previously predicted to take place after 30 years running of the TGP, and still the incision is accelerating ahead according to investigation. Mainly, because of regulations and also riverbed incision, water stages all way along the lowland reaches are lowered ahead of time by 2-4 m, that is the criminal leading the riparian shoals and major lakes, the Dongting and Poyang, dried up in advance, correspondingly. Also, because of earlier drying up and stage lowering, diversion of water from the river to the Dongting diminishes, the flow across Datong in Oct. is greatly reduced with the frequency of less than 15000 m³/s discharge greatly increased that is of key for the resisting of saltwater and the safety of drinking water for Shanghai. Moreover, at the same time of stage lowering, main channel flood level of specific discharge is elevated that means flood safety reduction. The present variation in runoff regime has changed the natural fluvial features and the environmental conditions in the lowland reaches and to low the impact of hydro-project should be listed as key restoration for the Yangtze River protection. We suggest to reposition the role of upstream hydro-projects to run the key reservoir firstly using to water as objecting goals, not electricity; to respect law-designated TGP principles of operation in its planning stage; to restore the sediment and other fluvial fluxes functionally via reservoir dredging; to strengthen the flood-coping capacity, in particular the flood detention requirement by the planning of the TGP to easy the tensions of both flood and refilling of water in autumn; and to improve the environmental conditions of the Yangtze connecting lakes, mainly through upstream reservoirs operation optimizations and it should also be supported through diverting more clear water from the river to Dongting Lake and improving the water supply facilities for Poyang Lake as auxiliary measures.