Abstract: Water pollution control based on water environment protection functional zones management is one of important works to solve the severe water pollution in China. The purpose,structure and features of water environment protection functional zones management information system under client/serve structure are summarized in this paper. Integrating related water environmental technology with network database,geographical information system,a decision support system serving the management of water environment in the water quality evaluation,statistics,inquiry and prediction is designed and established. Users can share the same information source while conducting different works. The efficiency of the management can be greatly improved by using this system.