Globally, the environmental contamination of stream sediments due to geogenic and anthropogenic sources is of growing concern. In this study, the heavy metals (Cd, Co, Cr, Cu, Ni, Pb, and Zn) in 22 superficial sediments in Wadi Asal, Red Sea, Egypt, were explored to assess sediment sources, the mobility of chemical species, and the degree of contamination in sediments. Therefore, the total heavy metal values in the fine fraction (< 63 μm), a five-step sequential extraction on selective samples, risk assessment, and principal component analysis (PCA) were applied. The mobility of heavy metals in Wadi Asal sediments, according to non-residual fraction percent, declines in the following order: Cd (90.9%) > Pb (85.2%) > Co (84.4%) > Cu (80.8%) > Zn (75.9%) > Ni (48.4%) > Cr (39.6%); indicating the high mobility of Cd, Zn, Pb, Cu, and Co. The mean metal contamination factor (CF) order is Cd (10.96) > Ni (3.91) > Cr (2.77) > Zn (2.18) > Pb (2.10) > Co (1.12) > Cu (0.70). The Geo-accumulation Index (Igeo) is decreased in the following order: Cd (2.19) > Ni (0.78) > Cr (0.55) > Zn (0.44) > Pb (0.42) > Co (0.22) > Cu (0.14). The risk assessment code (RAC) revealed very high to high risk for Cd, Co, and Pb. The results pointed out that the metals Cr, Co, Cu, and Ni are from geogenic sources, while Zn, Cd, and Pb are from anthropogenic sources due to Pb–Zn mining activities. Based on the threshold effect level (TEL), Cd, Cr, Ni, and Pb have adverse effects on living organisms. According to these findings, the area along Wadi Asal and the downstream regions on the beach are highly polluted and heavy metal monitoring in sediments and aquatic organisms is recommended.