Sources of neurotoxic mercury in forests are dominated by atmospheric gaseous elemental mercury (GEM) deposition, but a dearth of direct GEM exchange measurements causes major uncertainties about processes that determine GEM sinks. Here we present three years of forest-level GEM deposition measurements in a coniferous forest and a deciduous forest in northeastern USA, along with flux partitioning into canopy and forest floor contributions. Annual GEM deposition is 13.4 ± 0.80 μg m−2(coniferous forest) and 25.1 ± 2.4 μg m−2(deciduous forest) dominating mercury inputs (62 and 76% of total deposition). GEM uptake dominates in daytime during active vegetation periods and correlates with CO2assimilation, attributable to plant stomatal uptake of mercury. Non-stomatal GEM deposition occurs in the coniferous canopy during nights and to the forest floor in the deciduous forest and accounts for 24 and 39% of GEM deposition, respectively. Our study shows that GEM deposition includes various pathways and is highly ecosystem-specific, which complicates global constraints of terrestrial GEM sinks.