This paper introduces the method of data envelopment analysis (DEA) for evaluation of the degree of harmony between water resources and economic development of the water conservancy area of China’s South-to-North Water Diversion Project (SNWDP). For this evaluation, a super-efficiency DEA (SEDEA) model was developed based on the super-efficiency method. To verify the applicability of the SEDEA model, both the SEDEA model and a normal-efficiency DEA (NEDEA) model were used to evaluate the degree of harmony between water resources and economic development of typical cities in the SNWDP water conservancy area. The results show that the SEDEA model ranks the degree of harmony of typical cities more efficiently than the NEDEA model, and thus can better evaluate the degree of harmony between water resources and economic development of different cities than the NEDEA model.Furthermore, the SEDEA model can be applied as an operational research tool in regional water resources management.