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• Natural clay sediment from Riyadh exhibited highest surface area (288.5 m2 g−1). • Natural clay sediment from Medina and Al-Summan removed highest chlortetracycline. • pH range of 3.5–5.5 was optimum for CTC removal with natural clay sediments. • Interlayer sorption and electrostatic and H–π interactions were the sorption mechanisms. Natural clay sediments were collected from ten different localities in Saudi Arabia (S-1 from eastern, S-2 to S-4 from middle and S-5 to S-10 from western regions), characterized and evaluated for their efficiency towards chlortetracycline (CTC) removal from aqueous solutions. Sediment S-4 exhibited highest surface area (288.5 m2 g−1), followed by S-5, S-9, and S-1 (252.1, 249.6, and 110.4 m2 g−1, respectively). Sediments S-5, S-9, S-2, and S-4 showed the highest cation exchange capacities (CEC) (62.33, 56.54, 52.72, and 46.85 cmol kg−1, respectively). The pH range of 3.5–5.5 was optimum for the highest CTC removal. Freundlich model was best fitted to CTC sorption data (R2 = 0.96–0.99), followed by Dubinin-Radushkevich model (R2 = 0.89–0.97). The sediments S-4, S-5, and S-9 exhibited the highest CTC removal efficiency (98.80–99.05%), which could be due to higher smectite and kaolinite contents, CEC, surface area and layered structure. Post-sorption XRD patterns shown new peaks and peak shifts confirming the sorption of CTC. Electrostatic interactions, interlayer sorption and H–π bonding were the potential CTC sorption mechanisms. Therefore, natural clay sediments with high sorption capacities could efficiently remove CTC from contaminated aqueous media. [ABSTRACT FROM AUTHOR]