Water confinement in the hydrophobic nanopores of highly siliceous zeolite having MFI and CHA topology is investigated by high pressure manometry coupled to differential calorimetry. Surprisingly, the intrusion of water is endothermic for MFI but exothermic for CHA. This phase S transition depends on the geometry of the environment in which water is confined: channels (MFI) or cavities (CHA). The energy of intrusion is mainly governed by the change in the coordination of water molecules when they are forced to enter the nanopores and to adopt a weaker, hydrogen-bonded structure. At such a nanoscale, the properties of the molecules are governed strongly by geometrical restraints. This implies that the use of classical macroscopic equations such as Laplace-Washburn will have limitations at the molecular level.