We present the results of an infrared (IR) spectroscopic investigation of interfaces between two hydrophilic Si wafers bonded at low temperature. Multiple internal transmission IR spectra were recorded of the bonds, with different chemical pretreatments of Si surfaces employed before bonding. The analysis of IR spectra shows that the number of O-H and H-Si-O-x species at the interface depends strongly on the chemical pretreatment type, which determines the bonding energy. The annealing procedure used in the bonding process leads to dissociation of water molecules, oxidation of silicon st the interfaces, and diffusion of hydrogen into silicon oxide layer formed at the interface. The difference in bonding processes is discussed.