The collaborative governance of subsystems within a river basin can play a critical role in addressing challenges, such as water scarcity, soil erosion, flooding, sedimentation, and water pollution, to achieve sustainable utilization of water resources. However, the current literature only focuses on isolated observations of these subsystems, leading to uncertainty and water resource destruction. This paper examines the evolution of the collaborative governance of water resources, water conservancy facilities, and socio-economic systems through self-organization theory in the Xiangjiang River Basin, China. The coupling theory and gray Grey Model (1,1) model were utilized with panel data from 2000 to 2019 to assess and predict the governance synergies of five subsystems: natural water, water conservancy facilities, water resource development and utilization, ecological environment, and socio-economic systems. There are 22 indicators contributing to these subsystems that were selected. The results indicate an S-shaped trend in collaborative governance for water resources, water conservancy facilities, and socio-economic systems. The elements of each subsystem exhibit both synergistic and competitive relationships. The unpredictable precipitation triggers a butterfly effect, changing systemic governance coordination, which closely relates to developing the natural water subsystem. Effective water conservation and regulation of water conservancy facilities are the keys to improving water-use efficiency and safeguarding water ecology. This study provides insights into the collaborative governance among subsystems and the evolution of the water resources, water conservancy facilities, and socio-economic systems in the Xiangjiang River Basin to promote sustainable water resource utilization.