Based on the established evaluation indicator system of urban water system, evaluation indicator data collected from six typical pilot sponge cities were analyzed using a coupling coordination model to empirically examine the development status of coupling coordination of the water system of different cities. The key indicators were identified through grey correlation analysis, and a vector autoregression model was established to investigate the mechanism, through which these key indicators impact the development of coupling coordination of the water system. The findings indicate that the water system of the six cities has progressed from serious or moderate incoordination to coordination after the construction of sponge cities, and “sponging” reconstruction had better short-term effectiveness in southern pilot cities, including Wuhan, Shenzhen, and Shanghai, compared to northern pilot cities, including Jinan and Beijing. Furthermore, the coupling coordination degree between the water ecology and water security subsystems is found to be the highest, while river regulation rate and drinking water compliance rate exert fluctuating effects, alternatively impeding or promoting the interrelation between the two sub-systems. By contrast, the coupling coordination degree between the water resources and water culture subsystems is the weakest, while the number of official platform publicity exerts a significant and sustained positive effect on the relationship between the two sub-systems. Additionally, there is a need for further enhancement of the coupling coordination degree between the water resources and water environment subsystems, and the increases of water consumption per 10 000 yuan of GDP and sewage treatment rate have significant promoting but short-lived effects on the coordination between the two sub-systems.