Parasite communities have been shown to be structured by processes at scales ranging from continental to microhabitat, but few studies have simultaneously considered spatial and environmental variables, measured at different scales, to assess their relative influences on parasite abundance, species richness, and community similarity. Parasite abundance, diversity, and community similarity in Athabasca River trout-perch (Percopsis omiscomaycus) were examined in relation to water quality, substrate profile, metal and organic compound levels in water and sediment, and landscape use patterns at different scales, as well as distance among sites and upstream-downstream position along the river. Although species richness did not differ among sites, there were significant differences in abundance of individual taxa and community structure. We observed a shift from communities dominated by larval trematodes Diplostomum spp. to domination by gill monogeneans Urocleidus baldwini, followed by a reversion further downstream. Variations in the abundance of these taxa and of overall community similarity were strongly correlated with sediment hydrocarbons (alkanes and polycyclic aromatic hydrocarbons (PAHs)) as well as landscape use within 5 km of study sites. No correlations were noted with any other predictors, indicating that parasite populations and communities in this system were likely primarily influenced by habitat level and landscape-scale filters, rather than larger-scale processes such as distance decay or river continuum effects.