A comprehensive description of the energetic, conformational, and vibrational features of the two amino acids (AAs) with polar side chains, i.e., serine and threonine, in aqueous environment, is provided. To adequately analyze the side chain conformational flexibility of these amino acids, we resorted to quantum mechanical calculations with the use of density functional theory, which allowed the determination of the energetic features of these AAs through 236 clusters. Each cluster contains a zwitterionic AA surrounded by seven explicit water molecules. The obtained data could evidence the effect of the side chain conformational angle (χ(1) and χ(2)) as well as the location of water molecules on the energy landscapes of both AAs. Four of the lowest energy clusters of each AA, which give rise to distinct side chain conformations, were selected in order to reproduce the FT-IR and Raman spectra recorded in aqueous solutions and to assign the vibrational modes responsible of the main observed bands.