Plasma-treated and DI H2O rinsed oxide layers are commonly used in wafer bonding applications. Borosilicate glass (BSG) layers deposited by low-pressure chemical vapor deposition (LPCVD) treated with an O2 plasma in reactive ion etching (RIE) mode at 0.6 W/cm2 and rinsed with DI H2O readily bond to GaAs and Si. The chemical role of this pre-bonding treatment was investigated using attenuated total reflection Fourier transform infrared (ATR- FTIR) spectroscopy. The peak intensities for both the Si-O and B-O absorbance bands decreased in intensity as a result the plasma treatment consistent with the uniform sputter etching of BSG. The effect of changing the total plasma treatment time was investigated in terms of the total amount of material removed. Polarization-dependent ATR-FTIR revealed that the H2O/OH absorbance bands decreased in peak intensity with the OH groups preferentially oriented perpendicular to the sample surface after the plasma treatment. The subsequent DI H2O rinse restores the water to the surface while changing the surface BSG composition. ATR-FTIR studies suggest that for oxide compositions greater than 10 mole % B2O3, the top 4 nm of B2O3 was removed or leached from the oxide layer during the DI H2O rinse.