From the historic literature on the Idrija mercury mine, it is evident that part of the smelting and mining waste was dumped into the Idrijca River. This waste was transported downstream during floods. The amount of mercury which has accumulated in the alluvial sediments of the Idrijca River until the present was studied. Mapping of Holocene river terraces of the Idrijca River was performed in order to estimate the volume of the alluvial sediment. For the purpose of the assessment of the mercury concentration, we sampled the alluvial sediments on different levels and performed an analysis of variance. The greatest variability is between the floodplain and terraces inside the same alluvial plain. Considering this fact, which determined the methodology employed for calculation, we estimated that about 2029 tons of mercury is stored in the Idrijca River alluvial sediments.