We investigated structural changes of the magnetite (001) surface upon exposure to water vapor at pressures up to 10 mbar as well as upon exposure to atomic hydrogen using surface X-ray diffraction, scanning tunneling microscopy, infrared spectroscopy, and X-ray photoelectron spectroscopy. Following a full structural analysis, we found for both adsorbates that the surface is roughening on an atomic level, indicating significant 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 the subsurface cation vacancy reconstruction present after preparation under ultrahigh vacuum conditions. In the case of water vapor, the lifting process arises in a pressure range between 10-4 and 10-3 mbar. We also observe an enhanced reactivity of the atomic hydrogen exposed surface with carbon species from the residual gas even at ultrahigh vacuum conditions.