In sub-arctic and arctic regions mercury is an element of concern for both wildlife and humans. Over thousands of years large amounts of atmospherically deposited mercury, both from natural and anthropogenic sources, have been sequestered together with carbon in northern peatlands. Many of these peatlands are currently underlain by permafrost, which controls mire stability and hydrology. With the ongoing climate change there is concern that permafrost thawing will turn large areas of these northern peatlands from carbon/mercury-sinks into much wetter carbon/mercury-sources. Here we can show that such a change in mire structure in the sub-arctic Stordalen mire in northern Sweden actually is responsible for an increased export of mercury to the adjacent lake Inre Harrsjön. We also show that sediment mercury accumulation rates during a warm period in the pre-industrial past were higher than in the 1970s when atmospheric input peaked, indicating that in areas with permafrost, climate can have an effect on mercury loading to lakes as large as anthropogenic emissions. Thawing of permafrost and the subsequent export of carbon is a widespread phenomenon, and the projection is that it will increase even more in the near future. Together with our observations from Stordalen, this makes northern peatlands into a substantial source of mercury, at risk of being released into sensitive arctic freshwater and marine systems.