Molecular modeling techniques have been used to investigate the interaction of L-lysine in aqueous medium with silanol and methyl sites onto quartz substrates. The substrate effect has been studied for partially hydrophilic surfaces formed by silanol and methyl groups with a ratio of 1:5 and hydrophobic fully methylated surfaces. Molecular dynamics and static calculations indicate that L-lysine does not show any significant interaction with fully methylated surfaces, while its interaction with hydroxylated/methylated surfaces is dominated by electrostatic and H-bond terms. Accordingly, on fully methylated surfaces there is no preferential orientation of L-lysine with respect to the surface, while for hydroxylated/methylated surfaces the L-lysine-surface interaction mainly depends on the molecular orientation, with a preferred geometry involving the ammonium group pointing toward the silanol site. The structure of water shells around L-lysine molecules was shown to be strongly affected by the relative hydrophilic/hydrophobic character of the surfaces. In particular, the order is almost completely lost for partially hydrophilic surfaces, while well-defined hydration shells around L-lysine are obtained for hydrophobic surfaces.