Guangxi’s rapid urbanization and rising environmental pressures have made balanced water–ecology governance a core regional policy concern. Using annual data for prefecture-level cities in Guangxi, China, from 2004 to 2022, this study constructs an ecological indicator system encompassing “water resources–pollutants–clean governance” and conducts a comprehensive evaluation with a coupling-coordination diagnosis. Data sources included the Guangxi Statistical Yearbook, the China Environmental Statistical Yearbook, and relevant editions of the Guangxi Statistical Bulletin of National Economic and Social Development. Methodologically, indicators were first standardized via minimum–maximum scaling. Using the driver–pressure–state–impact–response framework, indicators were selected. Objective weights were determined through the criteria importance through the intercriteria correlation method. The technique for order preference by similarity to the ideal solution method was used to compute composite scores for the three subsystems. We then established models for the coupling degree (C) and coupling-coordination degree (D). Across 2004–2022, the D ranged from 0.458 to 0.798, indicating predominantly low-to-moderate coordination with discernible phase fluctuations rather than extreme imbalance. In 2022, the headline metrics were measured at 0.958 for C and 0.798 for D, representing the upper end of the observed coordination level over the sample period. Overall, urban ecological governance in Guangxi remained only partially coordinated during 2004–2022, although with episodic improvements. Policy pathways should prioritize high-weight, high-dispersion dimensions to enhance subsystem matching and raise coordination.