This study establishes a baseline for trace metal speciation in Qarun and Wadi El-Rayan lakes. A five-step sequential extraction procedure was applied for the speciation of the Fe, Mn, Zn, and Cu in sediment samples collected at Qarun and Wadi El-Rayan lakes. Mn and Cu were the most mobile metals, whereas the residue fraction maintained the highest concentrations of Zn and Fe (≈ 60 %). No significant differences in metal concentrations were detected in the sediments of each lake sites, despite of the large distance between them (P > 0.05). Hazardous discharge sources are responsible for the high accumulation of metals in the nonresidual fractions. Qarun Lake showed high mobility factor for all studied metals than Wadi El-Rayan lakes; as such, all the humans, plants, animals and the general biota within the vicinity of this aquatic system are quite vulnerable to the trace metal exposure. According to geoaccumulation index (I-geo), the studied sediments were practically uncontaminated by Fe and Mn and classified as uncontaminated to moderately contaminated with Cu in Qarun and Zn in Wadi El-Rayan lakes. The low values of load pollution index (<1), confirmed the unpolluted condition of the lakes' superficial sediments.