In the current era of rapid urban development, the environmental protection requirements in China are increasing day by day. One of the ecological and environmental protection measures is to carry out the governance of existing water systems, which has received more and more attention. A water system governance project in Shanghai is facing various difficulties and challenges, including poor connectivity, ecosystem damage, socio-economic impacts, large capital investment and complex engineering technology. Through in-depth research on these key and difficult points, and through the reasonable exploration, the targeted solutions can be proposed to effectively solve these difficulties, promote the smooth implementation of water system governance projects, and achieve the fundamental improvement of water environment and restoration of ecosystems, which provide the reference for the implementation of similar projects in Shanghai and other regions.