The Czech Republic was heavily industrialized in the second half of the 20th century but the associated emissions of Hg and S from coal burning were significantly reduced since the 1990s. We studied dissolved (filtered) stream water mercury (Hg) and dissolved organic carbon (DOC) concentrations at five catchments with contrasting Hg and S deposition histories in the Bohemian part of the Czech Republic. The median filtered Hg concentrations of stream water samples collected in hydrological years 2012 and 2013 from the five sites varied by an order of magnitude from 1.3 to 18.0 ng L^− 1. The Hg concentrations at individual catchments were strongly correlated with DOC concentrations r from 0.64 to 0.93 and with discharge r from 0.48 to 0.75. Annual export fluxes of filtered Hg from individual catchments ranged from 0.11 to 13.3 μg m^− 2 yr^− 1 and were highest at sites with the highest DOC export fluxes. However, the amount of Hg exported per unit DOC varied widely; the mean Hg/DOC ratio in stream water at the individual sites ranged from 0.28 to 0.90 ng mg^− 1. The highest stream Hg/DOC ratios occurred at sites Pluhův Bor and Jezeří which both are in the heavily polluted Black Triangle area. Stream Hg/DOC was inversely related to mineral and total soil pool Hg/C across the five sites. We explain this pattern by greater soil Hg retention due to inhibition of soil organic matter decomposition at the sites with low stream Hg/DOC and/or by precipitation of a metacinnabar (HgS) phase. Thus mobilization of Hg into streams from forest soils likely depends on combined effects of organic matter decomposition dynamics and HgS-like phase precipitation, which were both affected by Hg and S deposition histories.