The presented research work is devoted to the investigation of the adsorption properties of biologically active molecules in mesoporous silicas. In particular, the interaction of ibuprofen with unique hydrated and functionalized silica carriers is unraveled by means of DFT-D calculations and experimental NMR experiments. The effects of temperature, degree of hydration, and adsorption site have been analyzed in detail to provide a molecular scale description of the adsorption and vectorization of a well-known drug, ibuprofen, on functionalized silicas. We are capable to conclude that the hydrated state, by the presence of a monolayer of water surface molecules on silica, plays the starring role.