The current study aims to investigate the behavior of local and natural clays rich in smectite (Ghassoul) collected in the region of Fez (North-East of Morocco) and valorize it in order to eliminate the two cationic dyes, malachite green (MG) and basic yellow 28 (BY28), which are hazardous on the environment as a result of the human trail, from aqueous solutions and to understand better the adsorption mechanism at the clay/dyes interface. Batch experiments were done to evaluate the influence of operational factors on the adsorption process and were compared to the static research to clarify the adsorption process. In addition, the experimental data were analyzed by Langmuir and Freundlich isotherms to describe the adsorption equilibrium. The Langmuir model perfectly describes the equilibrium, with a correlation coefficient greater than 0.998 with a maximum adsorption capacity of 588 mg g−1 for BY28 and 500 mg g−1 for MG. The experimental data fit well according to the pseudo-second-order kinetic model with a correlation coefficient of 0.998. Density function theory (DFT/B3LYP) was used to interpret better the adsorption mechanism and experimental design (DOE/FFD) to determine the factors influencing this mechanism. Experimental analytical data and theoretical calculations by DOE showed that BY28 has a higher adsorption affinity than MG DFT modeling of the two molecules in their steady-state allowed us to determine the reactivity's origin, allowing both dyes to establish der walls bonds with the clay. The results of the present study show that Ghassoul, a stevensite-rich clay abundant in the Mediterranean coastline, America, and Asia, can be advantageously used as a low-cost adsorbent for dye removal from wastewater.