Progressive industrialisation and urbanisation in recent decades have dramatically affected the soil cover and led to significant changes in its properties, which inevitably affect the functioning of other components of the forest ecosystems. The total content of Pb, Cd, Zn, Fe, Cr, Cu, Ni, As, and Hg was studied in twenty-five plots at different heights in the topsoil (organic and humus horizons) formed from the Carpathian flysch in the area of the Silesian Beskids (Western Carpathians). The aim of this article is to analyse the spatial distribution of potentially toxic elements in the mountain forest topsoil in different types of plant communities and to determine the relationship between altitude and potentially toxic elements contamination. The soils studied are acidic or very acidic, with an average range of 3.8 (H2O) and 2.9 (KCl). Concentrations of the metals Cd, Zn, Fe, Cr, Cu, Ni, and Hg on the plots that were analysed are within the range of permissible standards for forest ecosystems in Poland, while Pb and As exceed the permissible standards for this type of ecosystem. Spearman’s rank correlation coefficient showed a high correlation between Fe–Cr (r(32) = 0.879, Pb-Hg r(32) = 0.772, Ni–Cr r(32) = 0.738, Zn-Cd r(32) = 0.734, and Cu-Hg r(32) = 0.743, and a moderate statistically significant positive correlation between Cu-Pb r(32) = 0.667 and As-Pb r(32) = 0.557. No correlation was found between altitude and the occurrence of potentially toxic elements. The geo-accumulation index (Igeo) index, on the other hand, indicates that Pb, As, and Cd have the highest impact on soil contamination in all study plots: it classifies soils from moderately to strongly polluted. The enrichment factor (EF) obtained for As and Hg indicates significant-to-very high enrichment in all areas studied. The potential ecological risk index (PLI) calculated for the sites indicates the existence of pollution in all areas examined. The highest risk categories (considerable to very high) are associated with cadmium and mercury.