Mercury (Hg) trophic transfer and bioaccumulation in fish from a mine-impacted, eutrophic lake were examined in relation to foraging habitat, trophic position, and size. Diet analysis indicated that there were clear ontogenetic shifts in foraging habitats and trophic position. Pelagic diet decreased and benthic diet increased with increasing fish length in bluegill, black crappie, inland silverside, and largemouth bass, whereas there was no shift for prickly sculpin or threadfin shad. Stable carbon isotope values (delta13C) were inversely related to the proportion of pelagic prey items in the diet, but there was no clear relationship with benthic foraging. There were distinct differences between pelagic and benthic prey basal delta13C values, with a range of approximately -28 per thousand in pelagic zooplankton to approximately -20 per thousand in benthic caddisflies. Profundal prey such as chironomid larvae had intermediate delta13C values of approximately -24 per thousand, reflecting the influence of pelagic detrital subsidies and suppressing the propagation of the benthic carbon isotope signal up the food chain. Fish total mercury (TotHg) concentrations varied with habitat-specific foraging, trophic position, and size; however, the relationships differed among species and ages. When controlling for the effects of species, length, and trophic position, TotHg and delta13C were positively correlated, indicating that Hg trophic transfer is linked to benthic foraging. When examined on a species-specific basis, TotHg was positively correlated with delta13C only for bluegill, largemouth bass, and threadfin shad. However, diet-based multiple regression analyses suggested that TotHg also increased with benthic foraging for inland silverside and black crappie. In both species, benthic prey items were dominated by chironomid larvae, explaining the discrepancy with delta13C. These results illustrate the importance of foraging habitat to Hg bioaccumulation and indicate that pelagic carbon can strongly subsidize the basal energy sources of benthic organisms.