Abstract Patterns of total Hg (THg) and methyl Hg (MeHg) biomagnification were investigated in six pairs of co-located lacustrine and marine food webs supporting a common predator, Arctic charr. Mercury biomagnification rates (the slope of log Hg concentration versus δ15N-inferred trophic level) did not differ significantly between the two feeding habitats for either THg or MeHg, but THg and MeHg concentrations at the base of the food web were higher in the lacustrine environment than in the marine environment. The proportion of THg as MeHg was related to trophic level, and the relationship was statistically similar in the lacustrine and marine habitats. The biomagnification rate of MeHg exceeded that of THg in both habitats. We conclude that the known difference in Hg concentration between anadromous and non-anadromous Arctic charr is driven by differential Hg concentrations at the base of the lacustrine and marine foodwebs, and not by differential biomagnification rates.