Purpose The interaction of mercury with organic matter was studied on three soils with distinct physical-chemical compositions (Fluvisol, Luvisol, and Chernozem) and three vermicomposts based on various bio-waste materials (digestate, kitchen waste with woodchips, and garden bio-waste). Materials and methods Laboratory batch experiments, in which organic matter composition was modeled by adding graded doses of vermicompost to individual soils, were carried out. The composition of organic matter in these vermicomposts was assessed via fractionation of humic acids, fulvic acids, hydrophilic compounds, and possible hydrophobic neutral organic matter. Furthermore, the samples were artificially contaminated with inorganic and organic mercury. Prepared samples were stored under constant temperature of 25°C. The incubation experiments lasted for 56 days, in which the samples were taken ten times. During the experiments, the changes in mercury mobile phase amount were observed, and the influence of the source of contamination was evaluated. Results and discussion The amount of mobile mercury increased and then decreased during the time. In most of the soils and vermicompost combinations, the content of mercury bound to the soil was stable after 21 days. The effects of the mercury source on the exchangeable portion of Hg in the soils were most obvious in samples without added vermicompost. Nevertheless, differences between mobile inorganic and organic forms of Hg were lower in the case of Fluvisol compared to other soils. Moreover, in this soil, the content of available mercury was higher than from others. Conclusions In general, the smallest differences between mobile inorganic and organic forms of Hg were observed in the case of soil with the highest content of organic matter. Also higher doses of vermicomposts decreased the amount of mercury mobile phase available. Additionally, the largest positive influence of vermicompost dose on Hg mobility was measured in soils combined with vermicompost with the highest portion of humic acids.