Data on the regional geochemical background and threshold values of heavy metals are required to establish anomalies and assess soil pollution. As a rule, the background values are the average contents of elements in natural undisturbed soils, or the threshold values for the study area, obtained by statistical methods. The aim of the study is to obtain geochemical threshold values of heavy metals in the soils of the Lower Don and the Taganrog Bay coast using different statistical approaches. A total of 86 topsoil samples were collected from the study area. The concentrations of Cr, Mn, Ni, Сu, Zn, As, Cd, and Pb were analyzed by X-ray fluorescence. The median element concentrations in the soils of the study area were consistent with world soil average and metal concentrations in background soils of protected area. Using a ‘geochemical’ approach is not suitable for this dataset because it does not take into account the natural variability of concentrations in different soil types. The Tukey inner fence method delivers estimates that do not detect outliers for Ni, As, Cd, and Pb. The ‘median + 2 median absolute deviations’ method was the most appropriate, as it consistently provided the most conservative background values.