Mercury (Hg) is a ubiquitous toxic metal that biomagnifies in food webs, and can reach high concentrations in top predators. Evaluating Hg biomagnification in Arctic marine food webs is critical for understanding Hg dynamics and estimating exposure to understudied fish and wildlife consumed by humans. The majority of studies conducted on Hg biomagnification in the Arctic have focused on pelagic food webs. Benthic and benthopelagic food webs in Arctic marine ecosystems also support many species of subsistence and commercial importance, and data are lacking for these systems. In this study, we investigated food web structure and Hg biomagnification for the benthic, pelagic, and benthopelagic marine food webs of inner Frobisher Bay in Nunavut. Stable isotope ratios of carbon (δ13C) and nitrogen (δ15N), as well as total (THg) and methyl (MeHg) mercury concentrations were measured in fish, invertebrates, and zooplankton. Biomagnification in each food web was quantified with Trophic Magnification Slopes (TMS) and Trophic Magnification Factors (TMF). The highest TMS and TMF values were exhibited by the benthopelagic food web (TMS = 0.201; TMF = 1.59), followed by the pelagic food web (TMS = 0.183; TMF = 1.52), and lastly the benthic food web (TMS = 0.079; TMF = 1.20), with δ15N explaining 88%, 79%, and 9% of variation in Hg concentrations, respectively. TMS and TMF values were generally low compared to other Arctic marine food webs. Results from food web structure analyses indicated that the benthic food web had the greatest trophic diversity, trophic redundancy, and largest isotopic niche area of all food webs studied. Greater food web complexity may thus result in reduced MeHg biomagnification, but further study is required. Acquiring Hg and food web structure data is critical for predicting the effects of climate-induced environmental change on Hg dynamics, especially in the context of Arctic marine ecosystems.