Numerous materials are employed for the removal of contaminants from wastewaters. However, the regeneration/reuse of these materials is still seldom practiced. Quantitative insights into intermolecular forces between the contaminants and the functional surfaces might aid the rational design of reusable materials. Here, we compare the efficacies of aliphatic (C8H18), aromatic (C6H6), and aromatic perfluorinated (C6F6) moieties at removing methylene blue (MB+) as a surrogate cationic dye from water. We employed density functional theory with an implicit polarizable continuum model for water to accurately determine the contributions of the solvent's electrostatics in the adsorption process. Our calculations pinpointed the relative contributions of π-π stacking, van der Waals complexation, hydrogen bonding, and cation-π interactions, predicting that MB+ would bind the strongest with C6F6 due to hydrogen bonding and the weakest with C8H18. Complementary laboratory experiments revealed that, despite the similar hydrophobicity of silica beads functionalized with Si-C8H17, Si-C6H5, and Si-C6F5 groups, as characterized by their water contact angles, the relative uptake of aqueous MB+ varied as Si-C6F5 (95%) > Si-C6H5 (35%) > Si-C8H17 (3%). This first principles-led experimental approach can be easily extended to other classes of dyes, thereby advancing the rational design of adsorbents.