After the accomplishment of Threegorges reservoir, a 30 meters high waterlevelfluctuating zone (WLFZ) will appear along with the both banks, and become a kind of seasonal humid ecosystem. According to the program to store water of Threegorges reservoir, the ecological and environmental problems which will probably appear in WLFZ are discussed such as formation of contaminated zone along both banks, appearance of epidemic diseases in reservoir (including Chongqing urban districts), aggravation of geologic disaster, injury of biodiversity and intensifying of ecosystem fragile, etc. To counter the causes, distributed features and trends of ecological and environmental problems existing probably in WLFZ of Threegorges reservoir, the authors put forward six items of corresponding countermeasures.