Understanding parasite distributional patterns is fundamental for elucidating host-parasite relationships. The genus Salmincola is an ectoparasitic copepod group specifically infecting freshwater salmonids. Considering their strong association with their hosts, we can predict that the distribution and prevalence (analogs to abundance) of Salmincola reflect host salmonids. An alternative hypothesis is that their distribution will be strongly affected by environmental factors like stream drift because they have a free-living stage with low swimming ability. If this is the case, we predict a longitudinal gradient with higher occurrence or infection levels in downstream areas. To estimate the relative strength among factors affecting infection levels, we investigated the distribution pattern of Salmincola sp. on wild white-spotted charr Salvelinus leucomaenis in a southern Hokkaido river system. Based on data from 19 sites across three seasons, we found that host density and flow velocity affected the prevalence of Salmincola. On the other hand, no longitudinal gradient was observed and the prevalence was extremely low in some fragmented habitats (i.e., above dams and waterfalls). This indicates some compensation mechanisms against unidirectional downstream dispersal. We found that parasite prevalence and intensity were much higher in large migratory (anadromous) fish and, therefore, hypothesize that long-distance upstream migration helps the redistribution and population persistence of parasites in upstream areas.