To achieve the sustainable development goals established by the United Nations in 2015, China has adopted a series of measures to promote the modernization of water conservancy. However, its construction in China is imbalanced across regions as the endowment of water resources and economic development are distinct. Consequently, it is important to assess the progress of and analyze the spatial heterogeneity of water conservancy modernization construction in China from the perspective of sustainable development goals (SDGs). In this study, 31 regions in China were selected, and data on water conservancy construction in these sampled regions (excluding Hong Kong, Macao, and Taiwan) were collected in 2018. The results show that there exists an imbalanced development in terms of the overall level and the index level. About 60% of the regions scored below the overall average score for China’s current modernization of water conservancy. The eastern areas presented a high level of modernization, while the central, northeast, and western areas showed comparable modernization of water conservancy, all of which lag behind eastern areas of China. Furthermore, China’s water conservancy modernization also presented a strong spatial autocorrelation, and there was at least one deficiency in 55% of the regions, with the rate of deficiencies emerging in the West being much higher than in other regions. In a nutshell, this study provides a novel framework that can be extended to evaluate the SDGs and the effectiveness of water governance in other countries.