Reduced atmospheric loading of mercury (Hg) can improve the environmental status of freshwaters and coastal ecosystems. Sparse data limit impact assessments of changes in atmospheric Hg on aquatic ecosystems. Here, a Hg budget is calculated for Norway by estimating fluxes of Hg in the environment. Atmospheric inputs (ca. 3.3 tonnes annually) are a factor 10 higher than riverine export to coastal areas, indicating considerable retention in soils and lakes. Environmental loading of Hg to surface waters was separated into headwater (=catchment) export of Hg and atmospheric Hg loadings, which were of similar size (0.2 to 0.3 tonnes), where atmospheric loadings were considered of higher certainty than headwater fluxes. Robust methods for estimations of headwater Hg export at the regional scale are lacking. Hg budgets for small headwater catchments are more reliable and valuable to assess the fate of atmospheric Hg, and the role of aquatic Hg retention. Continued monitoring of Hg in deposition, catchments, and rivers are needed to reduce uncertainties in environmental assessments, in addition to international collaboration.