Identifying dominant sources and distribution of potentially toxic elements (PTEs) in soils is vital for environmental protection. However, detailed data on the ecological risks posed by PTEs are still limited in Bosnia and Herzegovina (BiH). This research aimed to fill that gap by examining the distribution and pollution levels of nickel (Ni), zinc (Zn), copper (Cu), and lead (Pb) in agricultural soils across three geomorphological units in the northwestern region of BiH. The study involved analyzing 338 soil samples collected from 169 sites at two soil depths: the arable layer (0–25 cm) and the sub-arable layer (25–50 cm). The average PTE contents across the entire study area followed the increasing order: Cu < Pb < Zn < Ni. Notably, the total Ni content exceeded the allowed maximum in 65.4% of the analyzed soils, with the highest exceedance in unit I (80.0%), followed by unit II (57.4%) and unit III (44.3%). Conversely, the total contents of Zn, Cu, and Pb were predominantly below the permissible maximum, with over 98% of the samples within safe limits. The study also found a homogeneous vertical distribution of all elements across different soil depths and an absence of significant ecological risk according to applied criteria: geo-accumulation index (Igeo), pollution index (PI), and pollution load index (PLI). These findings collectively suggest the dominance of natural (geochemical) sources of examined PTEs in the soils of this region. In addition to valuable insights into the soil environmental quality, this research underscores the importance of ongoing monitoring and risk assessment to protect soil health.