The urbanization process causes the increase of impervious surface, changes the underlying surface, material and energy cycle, and profoundly affects the urban ecosystem. Based on the hydrological process model, we constructed an evaluation framework for water ecosystem services. Taking the Jiuxiang River basin in Nanjing as an example, this study evaluates the process of urban impervious surface growth and hydrological cycle changes from 2000 to 2015, and reveals the impact of urbanization on water ecosystem services. The results showed that the impervious surface of the Jiuxiang River Basin in Nanjing increased rapidly from 2000 to 2015, and the impervious surface density increased from low to high. In the past 15 years, water supply services in urbanized areas have increased by 23.2%, while water regulation services and supply services have decreased by more than 20%, increasing the risk of urban waterlogging. Rapid urbanization changes the flux and stock in the water cycle process of urban ecosystems, which is the mechanism that leads to the decline of water ecosystem regulation services, support services and cultural services. The evaluation framework and technical method of water ecosystem services proposed in this study can provide theoretical basis and technical reference for water ecosystem services research and urban water ecosystem restoration.