Based on the idea of water control in the new era proposed by General Secretary Xi Jinping, a research framework and an evaluation index system of water ecological civilization construction quality were constructed, and the “vertical and horizontal” grading method and exploratory spatial data analysis method were used to evaluate the temporal change and spatial evolution trends of water ecological civilization construction quality. The results show that the evolution of water ecological civilization construction quality from 2004 to 2020 could be divided into a slow shock period and a fast growth period, demonstrating a relatively stable upward trend on the whole, with “gradient evolution” and “midstream driving” characteristics; the water ecological civilization construction quality has the characteristics of spatial positive correlation, along with a phenomenon of urban agglomeration polarization, especially in the Yangtze River Delta; the period of Fourteenth Five-Year Plan is an important strategic opportunity period for the central and western regions in China to give play to their late-developing advantages, and it is particularly important to give play to the radiative driving effect of leading urban agglomerations such as the Yangtze River Delta and Beijing-Tianjin-Hebei agglomerations.