We investigated structural changes of the magnetite (001) surface upon exposureto water vapor at pressures up to 10mbar as well as upon exposure to atomic hydrogenusing surface X-ray diffraction, scanning tunneling microscopy, infrared spectroscopyand X-ray photoelectron spectroscopy. Following a full structural analysis, we foundfor both adsorbates, that the surface is roughening on an atomic level, indicating signif-icant iron diffusion at the surface and in the near-surface region at room temperature.We found that this process is accompanied for both adsorbates by a lifting of thesubsurface cation vacancy reconstruction present after preparation under ultra-highvacuum conditions. In the case of water vapor, the lifting process arises in a pressurerange between 10􀀀4 mbar and 10􀀀3 mbar. We also observe an enhanced reactivity ofthe atomic hydrogen exposed surface with carbon species from the residual gas evenat ultra-high vacuum conditions.