The greater Cairo region is the most populated area in Egypt. The aquatic environment of the Nile River in this area is being affected by industrial activities. The study of the molecular structure of sediment may provide a good trace for such changes. Both Fourier transform infrared spectroscopy (FT-IR) and density functional theory (DFT) were used to study the effect of industrial waste disposal south of Cairo on the molecular structure of Nile River sediment. Four seasonal samples were collected from six sites covering 75 km along the Nile River. Grain sizes of 200 μm, 125 μm, 65 μm, and 32 μm, respectively, were examined. The results indicate that hydrated aluminum hydroxide controls the distribution of organic matter in the different grain sizes. Furthermore, the hydration of phenol may take place in grain sizes lower than 200 μm, which is indicated by the OH stretching at 3550 cm<sup>−1</sup> and verified by the obtained model. The formation of metal carboxylate bonds at 1638 cm<sup>−1</sup> (asymmetric) and 1382 cm<sup>−1</sup> (symmetric) indicate the possible interaction between heavy metals and other organic structures, mainly humic substances.

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