Abstract: Papers in this special issue represent a part of research results from a Key Project of Knowledge Innovation Program ofChinese Academy of Sciences.The project focuses on dynamics of aquatic ecosystem and environmental changes of the ThreeGorges Reservoir (and its main tributaries)before and after water storage.Based on the 3-yearmonitoring and studying, this papergives a summary of the researches, including 5 parts:1)physicochemical changes of the waters before and after impoundment;2)aquatic community changes before and after impoundment ;3)eutrophication problem in the Three Gorges Reservoir ;4)continuously monitor and kinetics of a spring algal blooming ;5)some consideration and suggestion for further ecological studieson the Three Gorges Reservoir.