The supramolecular salt [H2pip]3[Ge(hedp)2]⋅14 H2O (1) [H2pip2+=piperazine cation C4H12N22+; hedp5−=deprotonated form of etidronic acid, C2H3P2O75−) is reported. This consists of an organic–inorganic hybrid hydrogen-bonded nanoporous framework, the internal surface of which acts as a template for the three-dimensional (3D) clustering of water molecules. The structure and molecular dynamics of this material are characterised by single-crystal X-ray diffraction, thermogravimetric analysis, Raman (H/D isotopic substitution) spectroscopy, and 2H solid-state (wide-line and MAS) NMR spectroscopy. Material 1 is shown to be unusual because 1) few nanoporous materials exhibit a well-organised 3D framework of water molecules, 2) it provides a unique opportunity to follow experimentally and to rationalise the deconstruction of a 3D water framework and 3) despite the fact that the hybrid framework is a supramolecular salt, the structure does not collapse after dehydration and the final material is crystalline.