Inaouen wadi is the second largest tributary of the Sebou river, one of Morocco’s major rivers, which holds significant economic and social importance. Unfortunately, this watercourse is severely impacted by pollution from various human activities, particularly industrial sources. However, available data on the presence of potentially toxic elements (PTEs) that could harm human health in this region remain limited. PTEs pose major environmental risks due to their toxicity, persistence, and bioaccumulation. This study aimed to assess the concentrations of PTEs in the sediments of Inaouen wadi and its main tributaries based on sediment samples collected from 12 locations in 2019. The concentrations of Cd, Pb, Cr, Ag, Al, Cu, Fe, and Zn were measured using inductively coupled plasma atomic emission spectroscopy (ICP–AES), and sediment contamination levels were evaluated using multiple indices: the enrichment factor (EF), the geo-accumulation index (Igeo), the potential ecological hazard index (RI), and the modified ecological risk index (MRI). The results indicate that concentrations of Pb, Cd, Cr, Cu, Fe, and Zn are significantly influenced by urban discharges, particularly at sites S1, S3, and S5 near the cities of Taza and Oued-Amlil. The maximum values recorded were 7.01 g/kg for Pb, 0.9 g/kg for Cd, 0.1 g/kg for Cr, 19.9 g/kg for Fe and 1.9 g/kg for Zn. The enrichment factor (EF) revealed anthropogenic sources of Fe and Pb, confirming the human origin of these elements. The geo-accumulation index (Igeo) showed that the areas around stations S1, S3, and S5 are highly contaminated by Pb, Cd, and Fe, a finding also supported by the MRI. The study identified potential ecological risks at stations S1, S3, and S5, highlighting the urgent need for improved pollution management practices to mitigate environmental risks.