From 2011 to 2019, mercury (Hg) stores and fluxes were studied in the small forested catchment Lesní potok (LES) in the central Czech Republic using the watershed mass balance approach together with internal measurements. Mean input fluxes of Hg via open bulk deposition, beech throughfall and spruce throughfall during the periodwere 2.9, 3.9 and 7.6 μg m−2 year−1, respectively. These values were considerably lower than corresponding deposition Hg fluxes reported in the early years of the 21st century from catchments in Germany. Current bulk precipitation inputs at unimpacted Czech mountainous sites were lower than those in Germany. The largest Hg inputs to the catchment were via litterfall, averaging 22.6 and 17.8 μg m−2 year−1 for beech and spruce stands. The average Hg input, based on the sum of mean litterfall and throughfall deposition, was 23.0 μg m−2 year−1, compared to the estimated Hg output in runoff of 0.5 μg m−2 year−1, which is low compared to other reported values. Thus, only ~2% of Hg input is exported in stream runoff. Stream water Hg was only weakly related to dissolved organic carbon (DOC) but both concentrations were positively correlated with water temperature. The estimated total soil Hg pool averaged 47.5 mg m−2, only 4% of which was in the O‐horizon. Thus Hg in the O‐horizon pool represents 72 years of deposition at the current input flux and 3800 years of export at the current runoff flux. Age‐dating by 14C suggested that organic soil contains Hg from recent deposition, while mineral soil at 40–80 cm depth contained 4400‐year old carbon, suggesting the soil had accumulated atmospheric Hg inputs through millennia to reach the highest soil Hg pool of the soil profile. These findings suggest that industrial era intensification of the Hg cycle is superimposed on a slower‐paced Hg cycle during most of the Holocene.