The key to the eco-environmental problem in the River Basin is water，which is the key inducement of ecosystem degradation in various regions of the basin. The restoration and protection of the water ecosystem in River basin not only depends on the self-regulation and self-organization ability of the ecosystem，but also needs the reasonable participation of human beings. This paper discusses the governance practice of three major water ecological problems in various basins，such as the reduction of Self-restraint function of source of water，the imbalance of relationship between water and sand，and serious water pollution. Based on this analysis，it analyzes and summarizes the constraints faced in River Basin water ecological restoration and governance，namely the difficulty of synergizing the relationship between water ecological governance and economic development in River Basin，the “tragedy of the commons” in the water ecological management，and the fact that existing laws and regulations cannot guarantee cross-regional effectiveness. Finally，this paper gives some countermeasures and suggestions for the pain points in the process of governance，in order to promote the high quality of water ecological protection in River Basin.