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Although land cover and meteorological conditions are known to impact mercury (Hg) deposition processes, few studies have addressed how changes in forest cover and shifting climatic conditions will impact the Hg cycle. The purpose of this study was to examine the effects of forest type (hardwood vs. conifer) and meteorological variation on atmospheric Hg deposition in two forest stands in Huntington Wildlife Forest in upstate New York, USA. Mercury deposition associated with litterfall was similar between the hardwood and conifer stands, but total Hg deposition was greater in the coniferous stand due to larger throughfall Hg. Soil evasion losses of Hg were significantly higher in the hardwood plot. Although Hg deposition was greater and evasion losses were lower in the conifer plot, soil Hg pools were smaller than in the hardwood plot. Annual variability in meteorological conditions was substantial between 2009 and 2010, and changes in Hg deposition over this period appear to be related to variation in temperature and precipitation quantity. The results from this study suggest that projected increases in temperature and precipitation in the northeastern United States could alter Hg deposition and availability by decreasing litterfall Hg inputs and increasing throughfall Hg inputs.