Abstract: Affected by economic and social activities, the Changjiang River Basin faces resource shortages, frequent pollution incidents, and soil erosion. The protection of water resources and ecological environment has become an urgent issue. Based on the theories of the "natural-social" dualistic water cycle, land-sea coordination, and the "Four Determinations by Water" (city, land, population, and production), an evaluation index system for the governance performance of coordinated management of "water resources, water environment and water ecology" ("Three Waters Coordination") was constructed, comprising five subsystems: the sustainability subsystem, barrier subsystem, conservation subsystem, economic subsystem, and social subsystem. The entropy-weighted TOPSIS model and the obstacle degree model were employed to analyze the spatio-temporal variations and influencing factors of the performance of "Three Waters Coordination" in 25 prefecture-level and above cities within the middle and lower reaches of the Changjiang River from 2008 to 2023. The results was follows: ① The average governance performance score in the middle and lower reaches of the Changjiang River was 0.162 4, which was at an upper-medium level. Specifically, the average score in the middle reaches (0.174 3) was slightly higher than that in the lower reaches (0.155 7), indicating marginally better governance performance, and both regions exhibited marked spatiotemporal disparities. ② Throughout the study period, the average annual growth rate of governance performance in the region remained generally positive, and the coefficient of range was relatively stable, showing a continuous upward trend in overall governance performance. Notably, Shanghai City consistently achieved high scores and outstanding performance, while Jiujiang, Ma′anshan, Hefei, and Nanchang City exhibited a fluctuating downward trend. ③ The ranking of obstacle degree for the main factors affecting governance was: conservation subsystem > social subsystem > barrier subsystem > economic subsystem > sustainability subsystem, and the dominant obstacle factors varied among cities. Based on these findings, region specific governance priorities are proposed, including restoring natural barriers, improving top-level design, and developing cloud-based management, thus providing a reference for water resource management, water ecological environment protection, and sustainable development in the middle and lower reaches of the Changjiang River.