As a primary pioneering region in China's ongoing urbanization process, the Yangtze River Economic Belt's (YREB's) urbanization process is itself continually accelerating, causing increasing pressure on the area's water ecosystem. It is necessary to examine the coordination relationship between the urbanization system and the water ecosystem in the YREB for realizing sustainable urban development. To this purpose, we use two comprehensive index systems, along with an improved coupling coordination degree (CCD) model. This method is used to analyze the coordination between urbanization and the water ecosystem across spatial gradients and temporal scales in the YREB, from 2008 to 2017. The factors acting as obstacles were diagnosed by utilizing the obstacle degree model. The results show that: (1) the coordination state of each region gradually improved during the 2008-2017 period. In terms of spatial distribution, the coordination state between two systems gradually increased from east to west. Moreover, the spatial differences across the 11 analyzed regions gradually narrowed with the passage of time. (2) The coordination between the two systems, from 2008 to 2017, evolved from a state of serious imbalance to a state of good coordination. The two systems passed from an initial period of imbalance or antagonism, coupled with rapid growth (2008-2011), through a period of basic coordination with steady growth (2011-2014), and finally toward a period of good coordination with slow growth (2014-2017). (3) Spatial urbanization and pressures on subsystems are the key factors acting as obstacles in the urbanization system and water ecosystem, respectively. Facing the process of rapid urbanization in China, the coupling analysis of the coordination between urbanization and the water ecosystem can help the government to formulate a reasonable new-type urban development strategy. This strategy will play an important role in China's sustainable urban development and water environmental protection. The findings of this study provide important support for urban planning in the future.