Stomach contents, parasite assemblages and morphometrics were compared in brook charr Salvelinus fontinalis from the littoral and pelagic zone of two adjacent lakes on the Canadian Shield. In lac Baie des Onze Îles, fish from the littoral zone had greater abundance of benthic prey in their stomach and were more heavily infected by parasites that use intermediate hosts associated with the littoral zone than fish captured in the pelagic zone. Littoral and pelagic brook charr from this lake also differed in regard to body shape and fin length, with each group being anatomically adapted to exploit their respective habitats. The highly significant correlation between morphometric and parasite canonical scores supports the hypothesis of functional diversification of individuals within lac Baie des Onze Îles. While fish from littoral and pelagic zones of lac Caribou did not differ in terms of diet, parasite assemblages or morphometrics, they were different to fish from lac Baie des Onze Îles in that they were less frequently infected with parasites that use gastropods as intermediate hosts, and had shorter pectoral fins. The inter-lake comparisons suggested that parasite assemblages and morphometrics of brook charr reflected the dominance of the limnetic and littoral habitats in lacs Caribou and lac Baie des Onze Îles, respectively.