The geochemical speciation of total mercury (THg) was examined in pre-1800 Arctic lake sediments to improve understanding of the factors controlling “natural baseline” THg. Solid-phase binding forms of THg were determined by sequential extraction of dated cores from three lakes in different ecozones (barren tundra, grassy tundra, and boreal forest). Sediment organic matter (OM) was mostly of algal origin. Mercury was highly concentrated in the sediment OM fraction (OM-Hg), comprising 60–87% of THg, while OM (as total organic carbon) constituted only 0.6–13% of sediment dry weight (DW). OM-Hg concentrations were equivalent to 159 ± 13 to 776 ± 215 ng Hg g−1 DW in algal OM and were enriched 2–39 times compared to sediment THg, indicating that even small changes in algal OM inputs could significantly alter THg. OM-Hg explained 76–96% of the variation in THg concentrations over many centuries. Concentrations of S2 carbon (an algal productivity proxy) and OM-Hg were significantly correlated in two lakes but not in the boreal forest lake possibly because of OM remineralization in its deep water column. Fluxes of S2 carbon, OM-Hg, and THg were highly correlated in the barren tundra lake but could not be calculated for the other lakes. The results overall indicate that high algal Hg concentrations due to scavenging of available Hg controlled OM-Hg flux to sediments, thus driving changes in THg concentrations and fluxes. These findings improve our understanding of the long-term stability of baseline THg in northern lakes under a changing climate, including in the modern era.