The main subject of this investigation was the assessment of the lithogenic and anthropogenic distribution of 69 elements in the sediments and fluvisol in the Bregalnica river basin. Alluvial soil and fluvisol samples were collected from the total of eighteen locations along the course of the Bregalnica river and additional thirteen samples were collected from its tributaries. The matrix elements accumulation patterns followed the order: Fe > Na > Al > Ca > Mg > K > Ti > P. The potentially toxic elements, such as As, Cd, Pb, and Zn, have enriched content in the sediments in the medium course of the river, where the main anthropogenic introduction activities occurred. By multivariate analysis the dominant geochemical associations were extracted, as follows: F1: Y-Eu-Lu-Cr-V-La-Gd-Nb-Co-Hf-Zr-Ga-Mg-Fe-Sr-Ta-Sn-Li-Na-RbNi-Ge-Be-Cs; F2: As-W-Ba-Ag-Cu-Tl-Zn-Sb-Mo-In-Cd-Te-Bi-Pb and F3: I-Sc-Br-K. Lead and zinc contents were strongly correlated with the hydrothermal exploitations, especially in the area of Neogene clastite and vulcanite. These elements occur as dominant geochemical markers of the anthropogenic impacts of polymetallic enrichments due to the hydrothermal ore exploitation (Factor 2). The impact of Oligocene volcanism (Kratovo-Zletovo region) was observed in the lithological enrichments of Pb, Zn, Cu, As, Sb, Mo and Bi. Despite the natural distribution along the course of the Bregalnica river, an exceptional anomaly in the iron distribution of the old polymetallic unused mineralization was detected in Zone 1 (Berovo region).