The sealing mechanism of silicon bonding interfaces is reported as a function of annealing temperature. Details of the structural and chemical interface evolution are obtained for hydrophilic silicon/silicon and silicon/silicon dioxide wafer bonding, using x-ray reflectivity and infrared spectroscopy. A two-step mechanism is demonstrated: first a partial sealing of the interface driven by cross-wafer silanol bond condensation and second a water evacuation via oxide formation at the silicon oxide interface.