We report here on atomic transport, thermal stability, and chemical evolution of HfSiO, HfSiN, and AlON films on Si(001), aiming at investigating the atomic scale behaviour of the involved chemical species, N and H in particular, when the films are submitted to usual thermal processing steps in inert and oxidizing atmospheres. The films were characterized by nuclear reaction analyses in resonant and non-resonant regions of the cross-section curves, X-ray photoelectron spectroscopy, and low energy ion scattering. The HfSiN/Si structure was shown to be more resistant to oxygen diffusion than HfSiO/Si, although the amounts of O incorporated in HfSiN/Si are larger than in HfSiO/Si. The main channel of oxygen incorporation is atomic exchange with nitrogen or oxygen atoms. HfSiN film on Si incorporate more hydrogen (or deuterium) and in more stable configurations than HfSiO/Si. Nitrogen incorporation into AlON films on Si renders this structure more stable against thermal annealing in vacuum and/or oxidizing atmospheres than Al2O3/Si.