Abstract: Under the context of vigorously promoting the construction of ecological civilization in China, Shenzhen and Hong Kong have entered the golden development period of the superposition of the Guangdong-Hong Kong-Macao Greater Bay Area and the Loop Shenzhen-Hong Kong Science and Technology Innovation Cooperation Zone. Standing at a new historical starting point, the urban water problem has become more and more prominent, and higher requirements have been put forward for water body harnessment. The Shenzhen River, as the boundary river between Shenzhen and Hong Kong, should serve as the model of cooperation between Guangdong, Hong Kong, and Macao, as well as the in-depth integration between Shenzhen and Hong Kong.This paper puts forward the concept and implementation plan for the comprehensive harnessment of the Shenzhen River Basin and the inadequacy of the current water works construction. At present, Shenzhen River needs to start from the aspects of basin coordination, flood control, and drainage, and establish a governance strategy of Shenzhen-Hong Kong collaboration, river bay linkage, and flood and waterlogging co-harnessment, providing a reference for the governance of boundary rivers.