Abstract: The Changjiang River Basin, a vital ecological and economic zone in China, faces challenges such as water scarcity, water environmental pollution, and fragmented watershed governance. Groundwater and surface water are closely interconnected through water exchange and pollutant transport, making single governance models insufficient for achieving resource optimization and ecological protection. The necessity for coordinated governance is evident in enhancing water resource utilization efficiency, ensuring ecological base flow, and preventing and controlling composite pollution. However, significant challenges persist, including the lack of specific laws and regulations, insufficient cross-departmental coordination, weaknesses in monitoring and remediation technologies, and conflicts of interest. Based on the water cycle coupling theory, system dynamics, and the integrated water resources management framework, this paper proposes: establishing a four-level governance system encompassing scientific understanding, process simulation, coordinated control, and policy management; adopting technical methods such as regional-site collaborative investigation, pollution pathway blocking, and water-soil remediation; strengthening intelligent monitoring and interdisciplinary research; improving policies and regulations for coordinated governance; establishing cross-regional coordination mechanisms; and enhancing public participation. These measures aim to achieve an overall improvement in the water environmental quality of the Changjiang River Basin.