High-quality and accurate environmental investigations are essential for the evaluation of contamination and subsequent decision-making processes. A combination of environmental geochemical indices, multivariate analyses and geographic information system approach was successfully used to assess contamination status and source apportionment of trace elements (Ag, As, Cd, Cr, Cu, Hg, Ni, Pb, Sb, V and Zn) in surface stream sediments from the Oued Rarai basin in north-western Tunisia, containing various metal and metalloid ores. The contamination level reported in this study indicates a non-negligible potential ecological risk, mainly related to sediment transport along the river. Antimony (concentrations ranged from 0.02 to 297 mg kg−1 and Igeo > 5), arsenic (from 0.5 to 1490 mg kg−1 and Igeo > 5), lead (from 2.9 to 5150 mg kg−1 and Igeo > 5) mercury (from 0.05 to 54.4 mg kg−1 and Igeo > 5) and silver (from 0.05 to 9.4 mg kg−1 and Igeo > 5) showed the most crucial contamination. Besides, potential ecological risk index values were maximum for arsenic with a median of 302, indicating a very high to serious ecological risk (> 160). Results from correlation analysis and principal component analysis revealed three main geochemical associations related to lithologic, tectonic and anthropogenic sources. V, Cr and Cu mainly originated from natural bedrock and soil. Ag and Cd were more controlled by both natural and mining enrichments. Mercury and Pb were mostly influenced by the ancient ore-related activities at the Oued Rarai site and north-east–south-west trending faults. Finally, Sb, As, Ni and Zn were largely controlled by the siliciclastic continental Neogene sequences. Finally, the physical and chemical dynamics of the watershed system, lithological properties, mineralisation, tectonic settings and mobilisation of subsurface sediments largely controlled both concentrations and spatial patterns of trace elements in the study basin. These results need to be considered in the strategies of suitable environmental management at former and current mining sites in north-western Tunisia.