The distribution of trace metals in active stream sediments from the mineralized Lom Basin has been evaluated. Fifty-five bottom sediments were collected and the mineralogical composition of six pulverized samples determined by XRD. The fine fraction (< 150 µm) was subjected to total digestion (HClO4 + HF + HCl) and analyzed for trace metals using a combination of ICP-MS and AAS analytical methods. Results show that the mineralogy of stream sediments is dominated by quartz (39–86%), phyllosilicates (0–45%) and feldspars (0–27%). Mean concentrations of the analyzed metals are low (e.g. As = 99.40 µg/kg, Zn = 573.24 µg/kg, V = 963.14 µg/kg and Cr = 763.93 µg/kg). Iron and Mn have significant average concentrations of 28.325 and 442 mg/kg, respectively. Background and threshold values of the trace metals were computed statistically to determine geochemical anomalies of geologic or anthropogenic origin, particularly mining activity. Factor analysis, applied on normalized data, identified three associations: Ni–Cr–V–Co–As–Se–pH, Cu–Zn–Hg–Pb–Cd–Sc and Fe–Mn. The first association is controlled by source geology and the neutral pH, the second by sulphide mineralization and the last by chemical weathering of ferromagnesian minerals. Spatial analysis reveals similar distribution trends for Co–Cr–V–Ni and Cu–Zn–Pb–Sc reflecting the lithology and sulphide mineralization in the basin. Relatively high levels of As were concordant with reported gold occurrences in the area while Fe and Mn distribution are consistent with their source from the Fe-bearing metamorphic rocks. These findings provide baseline geochemical values for common and parallel geological domains in the eastern region of Cameroon. Although this study shows that the stream sediments are not polluted, the evaluation of metal composition in environmental samples from abandoned and active mine sites for comparison and environmental health risk assessment is highly recommended.