Forest soils are among the world’s largest repositories for long-term accumulation of atmospherically deposited mercury (Hg), and understanding the potential for remobilization through gaseous emissions, aqueous dissolution and runoff, or erosive particulate transport to down-gradient aquatic ecosystems is critically important for projecting ecosystem recovery. Forestry operations, especially clear-cut logging where most of the vegetaiton is removed, can influence Hg mobility/fluxes, foodweb dynamics, and bioaccumulation processes. This paper measured surface-air Hg fluxes from catchments in the Pacific Northwest, USA, to determine if there is a difference between forested and logged catchments. These measurements were conducted as part of a larger project on the impact of forestry operations on Hg cycling which include measurements of water fluxes as well as impacts on biota. Surface-air Hg fluxes were measured using a commonly applied dynamic flux chamber (DFC) method that incorporated diel and seasonal variability in elemental Hg (Hg⁰) fluxes at multiple forested and harvested catchments. The results showed that the forested ecosystem had depositional Hg⁰ fluxes throughout most of the year (annual mean: −0.26 ng/m²/h). In contrast, the harvested catchments showed mostly emission of Hg⁰ (annual mean: 0.63 ng/m²/h). Differences in solar radiation reaching the soil was the primary driver resulting in a shift from net deposition to emission in harvested catchments. The surface-air Hg fluxes were larger than the fluxes to water as runoff and accounted for 97% of the differences in Hg sequestered in forested versus harvested catchments.