This study described methylmercury (MeHg) concentrations in a wide array of benthic invertebrates sampled from two locations in the Canadian Beaufort Sea (Arctic Ocean). I examined relationships between dietary indicators, specifically carbon, nitrogen and sulfur stable isotope ratios, fatty acid and fatty acid biomarker signatures, all in relation to MeHg concentrations of taxa identified using traditional taxonomy and genetic barcoding approaches. Methylmercury concentrations increased with trophic position (inferred from nitrogen stable isotope ratios), varied by feeding guild and were influenced by the type of energy sources supporting the food web. Higher MeHg concentrations were observed at a site closer to the outflow of the Mackenzie River. When accounting for the effect of feeding guild and dietary indicators, the results clearly indicated that location influenced MeHg accumulation in the benthic invertebrates. These results contribute valuable information for tracking MeHg dynamics in this region.