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The main objective of this work was to investigate the potential of Natural Safiot Clay (NSC), as an adsorbent for the removal of two cationic dyes such as Basic Blue 9 (BB9) and Basic Yellow 28 (BY28) from single and binary systems in aqueous solutions. For this, the effects of three factors controlling the adsorption process, such as initial dye concentration, adsorbent dose, and initial pH on the adsorption extent, were investigated and examined. The natural safiot clay was characterized using the following technique: energy-dispersive X-ray spectroscopy (EDX), scanning electron microscopy (SEM), DRX, and Fourier transform infrared (FT-IR) and pH of the point of zero charge (pHZPC). Energy-dispersive X-ray spectroscopy results indicate high percentages of Silica and Alumina. FT-IR spectrum identified kaolinite as the major mineral phase in the presence of quartz, calcite, and dolomite. The quantum theoretical study confirms the experimental results, through the study of the global and local reactivity and the electrophilicity power of the dyes. The electrophilicity power of dyes affects the removal efficiency. The theoretical study proves that BB9 (ω = 6.178) is more electrophilic than BY28 (ω = 2.480) and more interactions with surface sites. The results of the molecular dynamics simulation indicate that the dyes are adsorbed parallel to the surface of natural Safi clay (kaolinite), implying the strong interaction with the kaolinite atoms. All the results of quantum chemistry calculations and simulations of molecular dynamics are in perfect agreement with the results of the experimental study.