The Pannonian Basin System (PBS) and associated parts of the surrounding orogens (SOs) were selected for a regional geochemical mapping of concentrations of potentially toxic metals, with the sample media the topsoil horizon. Geochemical data form a sample space that is different from Euclidean, and therefore standard statistical methods are not applicable for such data. To apply standard statistical methods, data were transformed to Euclidean space by using a special case of an isometric log-ratio transformation for a composition consisting of two parts (the first part is the metal concentration of interest; the second part is the total concentration of all other elements in the composition). Estimations were performed using deterministic (Ordinary Kriging) and stochastic (sequential Gaussian simulations (SGS)) methods. The resulting maps provide insight into the distribution of certain metals in the PBS and associated parts of the SOs, and are intended to serve as base maps for further studies. The maps obtained with SGS provide additional information on the variability (uncertainty) of estimation.