The origin and bioavailability of nickel (Ni), chromium (Cr), and cobalt (Co) have been assessed in the Čemernica River basin among the following soil types: Leptosol on serpentinite and Fluvisol, Vertisol, and Leptosol on sandstone. Alongside the impact of serpentine rocks, part of the region also displays significant anthropogenic activity. A sequential analysis following the modified BCR procedure identified four fractions of heavy metals: F1—exchangeable and acid-soluble, F2—bound to Fe and Mn oxides, F3—bound to organic matter, and F4—residual. The overall content of Ni, Cr, and Co in the soil increases in the following order: Leptosol on sandstone, and Vertisol, Fluvisol, Leptosol on serpentinite. In most samples, the values exceed the maximum allowable concentrations in legal regulations, while in some samples, particularly in serpentine soils, they also exceed the remediation thresholds. The average contribution of nickel in the overall content decreases as follows: F4 > F2 > F3 > F1, chromium as F4 > F3 > F2 > F1, and cobalt in the most samples as F2 > F4 > F1 > F3. The percentage of Ni, Cr, and Co in the fractions of different soil types is similar to that in serpentine soils, though the absolute contents vary significantly, indicating a common origin, which is mostly geochemical. According to the Risk Assessment Code, most samples exhibit a low bioavailability risk.