The composition and diversity of parasite communities are useful tools to characterise ecosystem health and integrity. Environmental disturbances may affect parasite infection in fish directly, by their effects on the free-living stages, or indirectly, on the intermediate hosts. Slimy sculpins, Cottus cognatus, a small fish inhabiting cold waters of North America, have been considered as sentinels due to their limited mobility, often occupying relatively small areas throughout their lives and thus reflecting the local environment. Ninety-six specimens of C. cognatus were sampled from four tributaries of the Athabasca River to assess patterns of helminth parasite community structure in this fish and to study the composition and diversity of its parasite communities in relation to water quality. The localities included single samples from High Hills, Horse and Dunkirk rivers, and two from the Steepbank River. Twelve metazoan parasite species were found, most of them being larval forms. Significant differences occurred in the structure and composition of parasite assemblages of sculpins from the tributaries, although similarities were observed in connected and nearby sites. Parasite communities were influenced mainly by a combination of local environmental conditions, distance and connectivity, and were separated based on the distribution and abundance of autogenic and allogenic parasites. Water quality appeared to influence the distribution of trematode species that use gastropods as intermediate hosts, while proximity and connectivity of sites led to sharing allogenic parasite species in slimy sculpin.