In the Taihu Lake Basin, river system is well-developed and shallow lakes are dotted extensively. But the shallow lakes ecosystem function is degenerating, aquatic biodiversity is declining, the ability for purifying and intercepting pollutants is severely degrading. Due to the lakes characteristics of low-polluting water treatment capacity and favorable ecological environment for implementing all kinds of ecological remediation technology, the overall idea with ecological treatment for in-flow and out-flow rivers estuary, ecological remediation along the lakeside, restoration and stability of aquatic ecosystems as the main direction on the wetland reconstruction and ecological remediation in Taihu lake basin was put forward. A case study was conducted of the Gehu Lake which is a complicated and typical lake that linked to river in the headwater area of Taihu Lake Basin. It will provide a scientific basis for the ecological restoration and reconstruction of shallow lakes.