Taking Nanjing City as the research object, the evaluation index system for the utilization efficiency of water resources in Nanjing City is established. By using the DEA model based on the time series, the utilization efficiencies of water resources with and without consideration of the expected output are estimated. Through the comparison of the efficiency values of the two cases, it is found that under the environmental constraints, the utilization efficiency of water resources in Nanjing City considering the expected output is higher than that not considering the expected output. Therefore, by introducing the concept of environmental efficiency, the reasons are the work achievements and environmental efficiencies in the energy conservation and emissions reduction and environmental governance in Nanjing City.