Graphene oxide (GO) is the one of the most promising family of materials as atomically thin membranes for water-related molecular separation technologies due to its amphipathic nature and layered structure. Here, we show important aspects of GO on water adsorption from molecular dynamics (MD) simulations, in-situ X-ray diffraction (XRD) measurements, and ex-situ nuclear magnetic resonance (NMR) measurements. Although the MD simulations for GO and the reduced GO models revealed that the flexibility of the interlayer spacing could be attributed to the oxygen-functional groups of GO, the ultra-large GO model cannot well explain the observed swelling of GO from XRD experiments. Our MD simulations propose a realistic GO interlayer structure constructed by staggered stacking of flexible GO sheets, which can explain very well the swelling nature upon water adsorption. The transmission electron microscopic (TEM) observation also supports the non-regular staggered stacking structure of GO. Furthermore, we demonstrate the existence of the two distinct types of adsorbed water molecules in the staggered stacking: water bonded with hydrophilic functional groups and “free” mobile water. Finally, we show that the staggered stacking of GO plays a crucial role in H/D isotopic recognition in water adsorption, as well as the high mobility of water molecules.