Individual Arctic charr (Salvelinus alpinus) from Fjellfrøsvatn, northern Norway, could be categorized by their stomach contents as zooplanktivores or benthivores. Feeding specialization among these fish was evident from negative correlations between helminths transmitted by pelagic copepods (Diphyllobothrium dendriticum and D. ditremum) and those transmitted by the benthic amphipod Gammarus lacustris (Cystidicola farionis and Cyathocephalus truncatus). Occurrences of parasite species acquired from the same types of invertebrate were positively correlated in the fish. Strong relationships among habitat use, diet, and helminth infections among the Arctic charr indicated persistent foraging patterns involving long-term habitat use and feeding specialization. The distribution of all parasite species was highly aggregated in the fish samples, measured by the exponent k of the fitted negative binomial distributions (range: 0.5–7.5) and the variance-to-mean ratios (s2/x̄, range: 5–85). Charr specializing on either copepods or Gammarus predominantly contributed to high-intensity class intervals within the overall frequency distributions of the corresponding parasite species. Such fish had low infection intensities of helminths transmitted by other prey organisms. The detailed analyses of the parasite frequency distributions for fish with different habitat or feeding preferences evidently show how heterogeneity in trophic behavior contributes strongly to the commonly observed aggregation of helminths among hosts under natural conditions.