© 2016 Author(s). The energy difference between the oxide and bulk peaks in X-ray photoelectron spectroscopy (XPS) spectra was investigated for both GeO2/Ge and SiO2/Si structures with thickness-controlled water films. This was achieved by obtaining XPS spectra at various values of relative humidity (RH) of up to ∼15%. The increase in the energy shift is more significant for thermal GeO2on Ge than for thermal SiO2on Si above ∼10-4% RH, which is due to the larger amount of water molecules that infiltrate into the GeO2film to form hydroxyls. Analyzing the origins of this energy shift, we propose that the positive charging of a partially hydroxylated GeO2film, which is unrelated to X-ray irradiation, causes the larger energy shift for GeO2/Ge than for SiO2/Si. A possible microscopic mechanism of this intrinsic positive charging is the emission of electrons from adsorbed water species in the suboxide layer of the GeO2film to the Ge bulk, leaving immobile cations or positively charged states in the oxide. This may be related to the reported negative shift of flat band voltages in metal-oxide-semiconductor diodes with an air-exposed GeO2layer.