The influence of geomorphological factors to Hg contamination of the Idrijca River alluvial sediments because of the historical mining and ore roasting activities has been studied. Main source of Hg in alluvial sediments was dumping of ore roasting residues and mining waste into the river channel and its erosion downstream. The position of the material in relation to the geomorphological properties is highly related with its Hg content. Floodplains were found to be the most contaminated geomorphological units (mean Hg content 335 mg/kg), with Hg concentration rapidly dropping in the first terrace (155 mg/kg). The least contaminated material was found in the higher terraces (3.8 mg/kg). Sampling upstream Idrija (average Hg content is 22.1 mg/kg) shows that not only mine and ore roasting plant increased Hg levels in alluvial deposits but also contaminated sites upstream Idrija contribute to Hg contamination. Geochemical background for alluvial sediments for this area is estimated to be 0.75 mg/kg. Downstream Idrija, 9 hotspots were determined where highly contaminated material is actively eroded and carries a high risk of further contamination of the Soča River and northern Adriatic Sea ecosystems. ► Hg contamination of alluvial sediment because of mining tradition in Idrija. ► High rate of contamination, up to 2000 mg/kg, enrichment factors up to 15,000. ► Floodplain most contaminated geomorphological unit. ► Exponential decrease of contamination in relation to the distance from the source. ► Geochemical background for Hg in alluvial sediments estimated to 0.75 mg/kg.