Silicon wafer bonding is achieved by joining two particle‐free silicon wafers and annealing to elevated temperatures (∼1100 °C). We have used multiple internal transmission infrared absorption spectroscopy to probe the interface between the wafers upon initial joining and also during subsequent annealing steps. For atomically flat hydrophobic wafers (H passivated), we observe a pronounced shift in the Si–H stretching frequency due to the physical interaction (van der Waals attraction) that occurs when the surfaces come into intimate contact. The hydrogen eventually disappears at high temperatures (1000 °C) and Si–Si bonds are formed between the two surfaces. For hydrophilic wafers (oxide passivated), we initially observe three to five monolayers of water at the interface (providing the initial attraction through H bonding), as well as the presence of hydroxyl groups that terminate the oxide at low temperature. Upon moderate heating (<400 °C), the water trapped at the interface dissociates and leads to the formation of additional oxide. Between 400 and 800 °C, the hydroxyl groups disappear, resulting in a corresponding increase in oxideandthe formation of Si–O–Si bridging linkages across the two surfaces.