This study proposes schemes of GIS-based system development for integrated information management in water environment linked with Korean Reach File (KRF). For this purpose, precedent studies and systems of the U.S. were investigated and analyzed to induce optimal methodology for Korean circumstances. Thereafter, data linkage methods of KRF and Water Environment Information System (WEIS), system configuration plans, application development plans, and KRF improvement and maintenance plans were considered. For data linkage and system configuration, three methods were suggested: an overlay operation-based data linkage method, entering spatial addresses into the existing DB, and creating link information between KRF and the existing DB. The first method was predicted to be the most effective for system implementation, the second method is advantageous for search tasks, and the third method is advantageous for system security and maintenance. Various types of applications should be developed in the consideration of the types of the users and their usages. Moreover, there is a need for further research on regular renewal of KRF, standard development, expansion of construction areas, etc. Based on the present results, research on actual system design and development also should be conducted for supporting Total Maximum Daily Loads (TMDLs).