Effects of Boreal forest harvest on mercury (Hg) and methyl mercury (MeHg) soil pools and export by stream runoff were quantified by comparing 10 reference watersheds (REFs) covered by >80 year old Norway spruce (Picea abies Karst.) forests with 10 similar watersheds subjected to clear-cutting (CCs). While total Hg soil storage did not change, MeHg pools increased seven times (p = 0.006) in the organic topsoil 2 years after clear-cutting. In undulating terrain, situated above the postglacial marine limit (ML) of the ancient Baltic Sea, the mass ratio between flux-weighted MeHg and dissolved organic carbon (MeHg/DOC) in stream runoff increased 1.8 times (p < 0.004) as a consequence of forest harvest. When recalculated to 100% clear-cutting of the watershed, the annual MeHg stream export increased 3.8 times (p = 0.047). Below the ML, where the terrain was flatter, neither the MeHg/DOC ratio nor the annual export of MeHg differed between REFs and CCs, likely because of the larger contribution of MeHg exported from peaty soils and small wetlands. The most robust measure, MeHg/DOC, was used to calculate MeHg loadings to Boreal headwaters. If the forest harvest effect lasts 10 years, clear-cutting increases MeHg runoff by 12-20% in Sweden and 2% in the Boreal zone as a whole. In Sweden, having intensely managed forests, 37% and 56% of MeHg are exported from peatlands and forest soils, respectively, and forest clear-cutting is adding another 6.6%. In the Boreal zone as a whole peatlands and forests soils contribute with 53% and 46%, respectively, and clearcutting is estimated to add another 1.0%. An expected rapid increase in Boreal forest harvest and disturbance urge for inclusion of land use effects in mercury biogeochemical cycling models at different scales.