Clay minerals are increasingly used to remove dyes from wastewater. In recent times, computational simulation methods have become indispensable for investigating the adsorption mechanisms of dyes on clay surfaces at the molecular level. This study investigates the adsorption features of two acid dyes, namely acid blue 25 (AB25) and acid red 88 (AR88), on the (001) surface of kaolinite in an aqueous medium using density functional theory (DFT), Monte Carlo (MC), and molecular dynamics (MD) simulations. Quantum chemical parameters (QCPs) show that the AB25 molecule exhibits higher reactivity compared to the AR88 molecule. As well, analysis of the sigma profile reveals a moderate polarity of the two dye molecules studied in comparison with the water molecule. The low-energy adsorption configuration of AB25 and AR88 molecules show that each molecule is oriented parallel to the (001) surface of kaolinite over short distances. The adsorption energies indicate that the kaolinite (001) surface has high affinity towards AB25 in comparison with the AR88 molecule (Eads(AB25) = -926.01 Kcal.mol−1; Eads(AR88) = -742.08 Kcal.mol−1), which was supported by analysis of the self-diffusion coefficient (SDC) values (SDCAB25 = 7.79 × 10-10 m2.s−1; SDCAR88 = 1.4 × 10-9 m2.s−1). Additionally, calculation of the radial distribution function of the oxygen and nitrogen atoms of AB25 and AR88 molecules show the contribution of these atoms in the chemical interactions that take place with the (001) surface of kaolinite. The adsorption mechanism of the investigated dye molecules may be influenced by both donor–acceptor and van der Waals interactions. The theoretical results from this study could be useful for better understanding the adsorption mechanisms of other acid dyes on clay minerals.