Mabahiss Bay and Safaga Bay are two important ports along the Red Sea coast of Egypt. The present study is the first to monitor halogen concentrations in these two ports. Certain halogens (F, Cl, Br and I) in coastal waters and sediments exhibited different behaviors. Fluoride (1.92–8.31 mg/L and 0.34–1.24 mg/g), chloride (20.76–22.68 g/L and 0.38–8.31 mg/g), bromide (95.90–151.84 mg/l and 6.66–50.61 mg/g), and iodide (2.77–39.19 μg/L and 1.71–3.76 μg/g) appeared in the seawater and sediments of Mabahiss Bay, respectively. In Safaga Bay, F, Cl, Br and I yielded ranges of (1.80–10.15 mg/L and 0.14–0.74 mg/g), (21.47–22.57 g/L and 0.68–1.42 mg/g), (15.98–146.51 mg/L and 6.13–74.59 mg/g) in seawater and sediments, respectively. In Mabashis Bay exclusively, the bromide and iodide levels in seawater increased significantly, and the sediments were vice versa. The average fluoride value in the two ports' seawater was higher than that in the unpolluted Mediterranean Sea. In contrast, the average bromide content in Mabahiss Bay seawater exceeded the Mediterranean Sea level. The seawater chloride content of the two ports was within the Mediterranean seawater's value, but the iodide concentration was lower than that of the unpolluted seawater. The application of different multivariate statistical techniques showed that halogen's distribution and halogen's geochemical characteristics control interaction in each region, ground flux, and proximity to human sources.