Because of the dominant role of the surface of molecules and their individuality, molecules behave distinctively in a confined space, which has far-reaching implications in many physical, chemical, and biological systems. Here we demonstrate that graphene forms a unique atom-thick interstitial space that enables the study of molecular diffusion in two dimensions with underlying silica substrates. Raman spectroscopy visualized intercalation of water from the edge to the center underneath graphene in real time, which was dictated by the hydrophilicity of the substrates. In addition, graphene undergoes reversible deformation to conform to intercalating water clusters or islands. Atomic force microscopy confirmed that the interfacial water layer is only ca. 3.5 angstrom thick, corresponding to one bilayer unit of normal ice. This study also demonstrates that oxygen species responsible for the ubiquitous hole doping are located below graphene. In addition to serving as a transparent confining wall, graphene and possibly other two-dimensional materials can be used as an optical indicator sensitive to interfacial mass transport and charge transfer.