Water resources’ use efficiency is an important issue under China’s rapid economic growth. This is because some provinces’ economic development may be delayed due to lack of adequate water resources. Whereas, high economically developed provinces may overuse water resources in order to achieve their economic goals; while also creating a large amount of pollutants. To assess water resources’ use efficiency from the resampling super data envelopment analysis (DEA) approach, our research comprehensively utilizes the following as inputs and outputs: (1) water resources: supply of water (SW), per capita water consumption (PCWC), and total water resources (TWR); (2) economic development: gross domestic product (GDP); (3) environmental issues: governance wastewater investment (GWI), wastewater discharge (WD), chemical oxygen demand (COD), and other major pollutants (OMP). The results show that Tibet, Beijing, Guangdong, Qinghai, Shandong, Sichuan, Yunnan, Tianjin, Jiangsu, and Henan have relatively good water resources’ use efficiency with efficiency values larger than 1. The best efficiency is in 2015, while the worst is in 2017. Water resources’ use efficiency shows significant regional differences in 2013–2017, with the best average efficiency value in southwest China (1.4355) and the worst in north China (0.2987). The results of the Wilcoxon test present that PCWC, GDP, COD, and OMP exhibit very significant differences, PN and WD have significant differences, and SW and TWR have no significant influence. These results imply that China’s regional governments must formulate a better water resource strategy based on the water resource distribution of each region. Lastly, the emissions of environmental pollutants must be strictly monitored.
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