Based on 20 ecological variables (e.g., stream habitat morphology, body size, longevity, fecundity, mating system, diversity of food at trophic level, and distance from human activities), we evaluated the possibility of common species becoming endangered species in the Red List of the Ministry of Environment, Japan based on the ecological features of native freshwater fish in Japan. Of 109 common species distributed in Japan, 41 species (37.6%) are listed as endangered species. The results of logistic analysis showed that distance from human activities could be used as a valid variable to predict which species are likely to become endangered.