Catchment-scale variation between lake habitats has the potential to simultaneously influence the trophic niche and parasite community of fish hosts. In this study, we investigated the trophic niche and parasite community of sympatric Arctic charr and brown trout populations from two inter-connected southern Norwegian lakes at different altitudes. Arctic charr and brown trout occupied profundal and littoral habitats in each lake, respectively, whereas brown trout replaced Arctic charr in pelagic habitats of the lower altitude lake. Distinct between-lake differences in diet and parasite community composition were noted for brown trout; however, both fish species showed highly overlapping trophically transmitted parasite communities regardless of the habitats each species used. Our results suggest that environmental differences over relatively limited geographical distances have the potential to influence fish habitat use and parasite community structure.