A methodology for indexing river environmental condition was developed and applied to 269 subsections of national rivers located in the Republic of Korea, based on a river management perspective. The resulting index has been called the River Environment Index (REI). To develop the methodology, a total of 32 factors related to a river's environment were initially investigated, from which 16 were chosen based on their measurability, predictability, measurement regularity and obtainability. Then, using the analytical hierarchy process (AHP) and based on a survey of 62 river management experts in Korea, the weighting coefficient for each of the 16 factors was determined. Finally, the REI values were estimated by linearly combining the 16 measured factors for the 269 river subsections and mapped using a geospatial information system platform. We expect that the REI will be used to increase the efficient allocation of national budgets for environmentally-friendly river restoration projects of the country's national rivers. Through this new index, prioritization of these rivers will be made using an holistic river management perspective.