Abstract: In the headwater area of the Taihu Lake Basin,lakes are dotted extensively and linked to each other with rivers.A case study was conducted of the Gehu Lake-Taige Canal and Caoqiao River-Taihu Lake to explore characteristics,ecological status,and water environment pollution of the water system and major problems existing with the system.On such a basis,a pollution control program was put forth for waterbodies linking river and lake.Due to the dense water network and shallow lake in the Taihu Lake Basin,hydrological conditions and water pollutants in the environment under the river-lake linked are extensively explored in this study.The program includes the following strategies: intensify control of pollutants at the source,mitigate pollution load,and combine pollution control with ecological remediation,so as to raise the self-purification capacity of lakes and self-remediation capacity of the ecosystem;intercept pollutants and purify in-flowing rivers so as to ensure provision of clean water sources for in-coming rivers;manage various pollutant sources in watersheds of in-coming rivers and intercept and control pollutants alongside the river banks from coming into the in-coming rivers,so as to build up clean rivers and improve the natural purification capacity of in-coming rivers and hence to further reduce pollutants moving with the water of in-coming rivers;set up ecological interception projects at the joints of river and lake and other key waters to intensify purification of water off pollutions so as to further reduce pollutant flow into lakes;and implement system regulation and optimal configuration so as to construct a safety shelter system to control pollution and protect water environment of the Taihu Lake at its headwater areas.Migration,transformation and movement behavior of pollutants under above-mentioned conditions are the major scientific problems.Cooperative method and optimization plan of ecological regulation for waterbody treatment in the river-lake linked basin should be developed based on regional water shed characteristics and ecological environment issue.Meanwhile,the non-point pollutant from town and villages along the rivers are also the main control strategy.Rural domestic wastewater disposal should be conducted by using the solid waste as carrier under the conditions of the natural decomposition on pollutants.Pollutants degradation process was examined to the rate and mechanism for the ecosystem in the shallow lake under various hydraulic condition and main biological factors configuration.The self purification capacity of the scientific issues on the shallow lake must be addressed.