Very high levels of mercury (Hg) have recently been reported in marine mammals and other higher trophic-level biota in the Mackenzie Delta and Beaufort Sea of the western Arctic Ocean. To quantify the input of Hg (particulate, dissolved and methylated) by the Mackenzie River as a potential source for Hg in the ecosystem, surface water and sediment samples were taken from 79 sites in the lower Mackenzie Basin during three consecutive summers (2003-2005) and analyzed for Hg and methylmercury (MeHg). Intensive studies were also carried out in the Mackenzie Delta during the freshets of 2004 and 2005. Large seasonal and annual variations were found in Hg concentrations in the river, coincident with the variations in water discharge. Increased discharges during spring freshet and during the summers of 2003 and 2005 compared to 2004 were mirrored by higher Hg concentrations. The correlation between Hg concentration and riverflow suggests additional Hg sources during periods of high water, potentially from increased surface inundation and increased bank erosion. The increase in the Hg concentration with increasing water discharge amplifies the annual Hg and MeHg fluxes during high water level years. For the period 2003-2005, the Hg and MeHg fluxes from the Mackenzie River to the Beaufort Sea averaged 2.2 tonnes/yr and 15 kg/yr, respectively, the largest known Hg source to the Beaufort Sea. More than half of the mercury flux occurs during the short spring freshet season which coincides with the period of rapid growth of marine biota. Consequently, the Mackenzie River input potentially provides the major mercury source to marine mammals of the Beaufort Sea. The Hg and MeHg fluxes from the Mackenzie River are expected to further increase with the projected climate warming in the Mackenzie Basin.