The elastic and structural behavior of natural cordierite compressed in aqueous medium up to 6 GPa was studied by means of in situ synchrotron powder diffraction with a diamond-anvil cell. In the range between 1–4 GPa the elastic behavior is regular and slightly anisotropic, with linear compressibilities βa:βb:βc = 4:4:5, the most rigid a–b plane coinciding with the orientation of 6-membered rings. A distinct decrease of compressibility in the range of 4–5 GPa indicates a pressure-induced hydration (PIH), which is confirmed by the structure refinements. The addition of about 60% of the initial water content into the cordierite channels proceeds through positional disordering of the H2O sites inside the channel cavity and a stepwise filling of the H2O position inside the 6-membered rings, leading to the phase transition at about 4.7 GPa. The appearance of H2O molecules inside 6-membered rings prevents their contraction and even causes their slight enlargement along the a direction, apparently related to the orientation of H-bonds. This results in an anisotropic deformation of the unit cell and an increase of the a parameter in the HP phase at 4.9 GPa, as well as a decrease of linear compressibility along a upon the further compression up to 6 GPa (βa:βb:βc = 5:9:10).