This study investigates the adsorption of caffeine in water on organically modified clays (a natural montmorillonite and synthetic saponite, which are smectite group of layered clay minerals). The organoclays were prepared by cation-exchange reactions of benzylammonium and neostigmine with interlayer exchangeable cations in the clay minerals. Although less caffeine was uptaken on neostigmine-modified clays than on raw clay minerals, uptake was increased by adding benzylammonium to the clays. The adsorption equilibrium constant was considerably higher on benzylammonium-modified saponite (containing small quantities of intercalated benzylammonium) than on its montmorillonite counterpart. These observations suggest that decreasing the size and number of intercalated cations enlarges the siloxane surface area available for caffeine adsorption. When the benzylammonium-smectite powders were immersed in water, the intercalated water molecules expanded the interlayer space. Addition of caffeine to the aqueous dispersion further expanded the benzylammonium-montmorillonite system but showed no effect on benzylammonium-saponite. We assume that intercalated water molecules were exchanged with caffeine molecules. By intercalating benzylammonium into smectites, we have potentially created an adaptable two-dimensional nanospace that sequesters caffeine from aqueous media.