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Huaihe River Basin is a unique region in China with high densities in both population and water projects (dams and floodgates) and is also subject to the most serious water pollution. It is a complicated water system, with a large number of tributaries, many inter-provincial rivers, and highly artificial river water control. Management of water projects regulating of river network require a series of professional analysis tools, which are closely related to the spatial modality and spatial distribution. In this paper, we apply GIS network analysis technology to water pollution tracing under water projects regulation, which establish digital river network model and integrate and manage water projects regulating related data resource. The study has put forward a water pollution management model as a GIS tool in the long-term water projects regulating process and pollution control plan for the Huaihe River Basin.