Polycation conformation upon adsorption to a negatively charged surface can be modulated by its charge density. At high charge density monomers directly interact with the surface in a ‘trains’ conformation and as charge density decreases a high degree of monomers dangle into solution in a ‘loops and tails’ conformation. In this study, the conformations of polycations upon adsorption to montmorillonite, as a function of polycation charge (20, 50 and 100% of the monomers, denoted as P-Q20, P-Q50 and P-Q100) were characterized and in accordance with their conformation, the adsorption of non-ionic and anionic molecules by the composite was tested. As expected, the adsorption of the nonionic pharmaceuticals increased to a composite with a ‘loops and tails’ conformation, due to both conformation and chemical properties. On the other hand, the anionic molecules, gemfibrozil and diclofenac, preferably adsorbed to composites with higher charge density (Q50 or Q100 composites). However, they showed different tendency toward the composites, i.e. higher adsorption of diclofenac by Q100 composite vs. higher adsorption of gemfibrozil by Q50 composite. To elucidate the differences in adsorption between these two pharmaceuticals, density functional theory calculations were employed. Both gemfibrozil and diclofenac were found to be better stabilized by methyl pyridinium sites (prevail in Q100 composite). The preferable adsorption of gemfibrozil by Q50 composite was explained by the presence of ‘loops and tails’ conformation enabling additional adsorption sites and diverse monomer-target molecule orientations.