Using the super-efficiency-DEA method, an index system is established from the perspective of inputs and outputs combined with the goal of water conservancy modernization in Jiangsu Province. By taking the contribution rate of water conservancy investment to the local GDP as the output indices, the water use efficiencies in 13 cities of Jiangsu Province in 2011 are evaluated and sorted. The effective or ineffective reasons of the DEA method are analyzed, and the corresponding countermeasures and suggestions are proposed.