Long-term observations at Arctic sites (Alert and Zeppelin) show large interannual variability (IAV) in atmospheric mercury (Hg), implying a strong sensitivity of Hg to environmental factors and potentially to climate change. We use the GEOS-Chem global biogeochemical Hg model to interpret these observations and identify the principal drivers of spring and summer IAV in the Arctic atmosphere and surface ocean from 1979–2008. The model has moderate skill in simulating the observed atmospheric IAV at the two sites (r ~ 0.4) and successfully reproduces a long-term shift at Alert in the timing of the spring minimum from May to April (r = 0.7). Principal component analysis indicates that much of the IAV in the model can be explained by a single climate mode with high temperatures, low sea ice fraction, low cloudiness, and shallow boundary layer. This mode drives decreased bromine-driven deposition in spring and increased ocean evasion in summer. In the Arctic surface ocean, we find that the IAV for modeled total Hg is dominated by the meltwater flux of Hg previously deposited to sea ice, which is largest in years with high solar radiation (clear skies) and cold spring air temperature. Climate change in the Arctic is projected to result in increased cloudiness and strong warming in spring, which may thus lead to decreased Hg inputs to the Arctic Ocean. The effect of climate change on Hg discharges from Arctic rivers remains a major source of uncertainty.