Abstract The Canadian Arctic has vast freshwater resources, and fish are important in the diet of many Northerners. Mercury is a contaminant of concern because of its potential toxicity and elevated bioaccumulation in some fish populations. Over the last decade, significant advances have been made in characterizing the cycling and fate of mercury in these freshwater environments. Large amounts of new data on concentrations, speciation and fluxes of Hg are provided and summarized for water and sediment, which were virtually absent for the Canadian Arctic a decade ago. The biogeochemical processes that control the speciation of mercury remain poorly resolved, including the sites and controls of methylmercury production. Food web studies have examined the roles of Hg uptake, trophic transfer, and diet for Hg bioaccumulation in fish, and, in particular, advances have been made in identifying determinants of mercury levels in lake-dwelling and sea-run forms of Arctic char. In a comparison of common freshwater fish species that were sampled across the Canadian Arctic between 2002 and 2009, no geographic patterns or regional hotspots were evident. Over the last two to four decades, Hg concentrations have increased in some monitored populations of fish in the Mackenzie River Basin while other populations from the Yukon and Nunavut showed no change or a slight decline. The different Hg trends indicate that the drivers of temporal change may be regional or habitat-specific. The Canadian Arctic is undergoing profound environmental change, and preliminary evidence suggests that it may be impacting the cycling and bioaccumulation of mercury. Further research is needed to investigate climate change impacts on the Hg cycle as well as biogeochemical controls of methylmercury production and the processes leading to increasing Hg levels in some fish populations in the Canadian Arctic.