In a warming climate, mercury (Hg) pathways in the Arctic can be expected to be affected. The Hg transport from the high arctic Zackenberg River Basin was assessed in 2009 in order to describe and estimate the mercury transported from land to the marine environment. A total of 95 water samples were acquired and filtered (0.4 μm pore size), and Hg concentrations were determined in both the filtered water and in the sediment. A range of other elements were also measured in the water samples. Hg concentrations in the filtered water were in general highest in the beginning of the season when the water came mainly from melted snow. THg concentrations in the sediment were in general relatively constant or slightly decreasing until mid-August, where after the concentrations increased. A principal component analysis separated the samples into spring, summer and autumn samples indicating seasonal characteristics of the patterns of element concentrations. The total amount of Hg in the sediment transported was estimated to 2.6 kg. Approximately 60% of the sediment-transported Hg occurred during a 24-h flood in the beginning of August caused by a glacial lake outburst flood. The total amount of transported dissolved Hg was estimated to 46 g, and 13% of this transport occurred during the 24-h flood. If it is assumed that the Hg transport by Zackenberg River is representative for the general glacial rivers in East Greenland, the total Hg transport into the North Atlantic from Greenland alone is approximately 4.6 tons year^-1 with an estimated annual freshwater discharge of ∼440 km³.