The Labrador Sea links the Arctic and North Atlantic oceans and constitutes one of the main entrances of atmospheric inputs into the Ocean's interior. We report here the first high-resolution Hg distribution pattern along a transect from Greenland to Labrador coasts sampled after the 2014 winter convection. Total Hg concentrations in unfiltered (HgTUNF) samples ranged from 0.25 pmol L− 1 to 0.67 pmol L− 1 averaging 0.44 ± 0.10 pmol L− 1 (n = 113, 1σ). Concentrations in filtered samples (HgTF, < 0.45 μm) represented from 62 to 92% of the HgTUNF and exhibited a similar distribution. High HgTUNF concentrations were found (i) in the waters of the Labrador Current, which receive desalted waters from the Canadian Arctic Archipelago, and (ii) in the waters over the Labrador shelf and rise. In the Labrador Sea Waters formed during the 2014 winter convection, HgTUNF concentrations were low (0.38 ± 0.05 pmol L− 1, n = 23), and increased gradually with depth (up to > 0.5 pmol L− 1) in the Northeast Atlantic Deep Waters. HgTF correlates with apparent oxygen utilization implying that atmospheric deposition, biological uptake, and microbial respiration control the Hg distribution in the Labrador Sea. Subtracting the amount of Hg released during organic matter remineralization allows us to identify a Hg and organic matter enriched fraction, which originates from fluvial sources in the Canadian Arctic Archipelago waters. This fraction is transferred southward, in surface waters with the Labrador Current, and at depth with the lower limb of the Atlantic Meridional Overturning Circulation. Climate warming, which will increase the mobilization of Hg from thawing permafrost, would consequently increase the Arctic export of Hg initially associated with organic matter.