A surface characterization study using x-ray photoelectron spectroscopy (XPS) and ion scattering spectroscopy has been performed on solvent-cleaned, n-type GaAs(001) substrates before and after room temperature exposure to the Aux produced by a novel atomic hydrogen source based on electron-stimulated desorption of hyperthermal (similar to 1 eV) hydrogen atoms. The native oxide layer on the solvent-cleaned GaAs(001) substrate contains C, As2O5, As2O3, and Ga2O3 according to the XPS data with Ga2O3 being the predominant species. Before H atom exposure, the C is present as hydrocarbons, carbonates, alcohols, and carbides with hydrocarbons as the predominant chemical stale. Upon room temperature exposure to a 1 eV hyperthermal H atom flux, the O in As and Ga oxides is removed, and the amount of C present is reduced through methane formation and desorption. In this process hydrocarbons are not converted to carbides, which are difficult to remove, as in the case of ion sputtering. After reduction the predominant form of O is a subsurface, dissolved O, and the outermost atomic layer is enriched in O by a chemical-induced driving force.