We assessed the naturalness of rivers based on the riparian vegetation index throughout the national territory of South Korea as a preparatory process for restoration to improve the ecological quality of rivers. The riparian vegetation index was obtained by incorporating the diversity of species and community, vegetation profile, and ratios of the number of species and areas occupied by exotic, obligate upland, and annual plants. The evaluation was conducted based on both the riparian vegetation index and each vegetation component. The result of the evaluation based on the riparian vegetation index showed that more than 70% of the river reaches were graded as less than “moderate” and exotic and obligate upland plants were more common than endemic aquatic plants. The reaches recorded as “very good” and “good” grades were usually restricted around the upstream of the north and central-eastern parts, whereas reaches of the other areas showed “poor” naturalness (less than “moderate”). The vegetation components selected for the evaluation showed a significant correlation with each other as well as the riparian vegetation index. The degree of contribution of each vegetation component showed that the vegetation profile played the most significant role, followed by species diversity, community diversity, and the ratio of area occupied by annual plants. The riparian vegetation index revealed a significant correlation with the indices based on other taxa such as benthic invertebrates, periphytic algae, and fish, habitat conditions in the waterway, and water quality based on biochemical oxygen demand (BOD). The diagnostic evaluation results imply that most reaches need ecological restoration. The reference information was prepared by incorporating the vegetation condition with the highest score in each reach in the diagnostic evaluation. The river reach was divided into five reaches of upper and lower valley streams, upstream, midstream, and downstream. Information on the reference vegetation for restoration was prepared with the stand profile including both horizontal and vertical arrangements of riparian vegetation and species composition classified by the reach divided into five types. The levels of restoration were determined based on the diagnostic evaluation results. The lower the naturalness grade, the higher the level of restorative treatment was recommended.