Based on extensive sampling of the rivers, troposphere, seawater and sediments, mercury (Hg) mass budgets are constructed for both contemporary and preindustrial times in the Hudson Bay Marine System (HBS) to probe sources and pathways of Hg and their responses to the projected climate change. The contemporary total Hg inventory in the HBS is estimated to be 98 t, about 1% of which is present in the biotic systems and the remainder in the abiotic systems. The total contemporary Hg influx and outflux, around 6.3 t/yr each, represent a 2-fold increase from the preindustrial fluxes. The most notable changes are in the atmospheric flux, which has gone from a nearly neutral (0.1 t/yr) to source term (1.5 t/yr), increased river inputs (which may also reflect increased atmospheric deposition to the HBS watershed) and in the sedimentary burial flux which has increased by 2.4 t/yr over preindustrial values, implying that much of the modern Hg loading entering this system is buried in the sediments. The capacity to drive increased Hg loading from the atmosphere to sediment burial may be supported by the resuspension of an extraordinarily large flux (120 Mt/yr) of shallow water glacigenic sediments uncontaminated by anthropogenic Hg, which could scavenge Hg from the water column before being transported to the deeper accumulative basins. Under the projected climate warming in the region, the rate of the sediment recycling pump will likely increase due to enhanced Hg scavenging by increasing biological productivity, and thus strengthen atmosphere-ocean Hg exchanges in the HBS.