After the recent success of several river rehabilitation projects including the Cheong-gye river case, a large number of local governments have been promoting their own projects in Korea. Most of the projects are aimed at securing the soundness of aquatic ecosystems according to the guidelines presented by the Korea Ministry of Environment. However, there is no clear guidance for the management goals of water quality and quantity. In this study, we have made an attempt to construct a habitat database (DB) for each domestic freshwater fish species. The fish population, and physical and physicochemical properties of the habitat of 70 domestic freshwater fish species were investigated using field monitoring data. After the statistical processing, the inhabitable range and optimal range of each species were suggested. Furthermore, based on the DB, a decision support system for ecological river restoration and rehabilitation has been developed, and applied for field tests. It became clear that the decision support procedure based on the fish habitat DB is useful in the planning stage of river rehabilitation projects to select the flagship fish, to decide the restoration goals considering their appropriate habitat and to suggest the optimum quantitative combination of each available water resource.