Abstract: The social demand of basin water environment research is analysed, the orientation and main research directions of the Water Environment Department are expounded, and the main research achievements during the last 5 years since the Department was established are presented. The main research work and innovations are summarized in 6 aspects: 1). technologies of treating eutrophication and algae of lakes and reservoirs; 2). assessment and countermeasures of the eco-environmental impact of rural hydropower projects; 3). methods of calculating and assessing pollution carrying capacity of rivers and lakes; 4). influence of reservoir on the continuous transport of water-sediment and nutrients and its ecological response mechanism; 5). treatment and ecological restoration technologies for water and soil polluted by heavy metals or environmental hormone; 6). technologies of groundwater pollution treatment. Finally the prospects of several crucial research fields for the Yangtze River management are discussed.