A detailed experimental and theoretical vibrational analysis of hydrogels of β-cyclodextrin nanosponges (β-CDNS), obtained by polymerization of β-cyclodextrin (β-CD) with the cross-linking agent ethylenediaminetetraacetic acid (EDTA) is here reported. A thorough structural characterization is achieved by exploiting the complementary selection rules of FTIR-ATR and Raman spectroscopies and by supporting the spectral assignements by DFT calculation of the spectral profiles. The combined analysis of the FTIR-ATR spectra of the polymers hydrated with H2O and D2O allowed to isolate the HOH bending of water molecules not involved in symmetrical, tetrahedral environments. The analysis of the HOH bending mode was carried out as a function of temperature, showing the existence of a supercooled state of the water molecules. The highest level of cooperativity of the hydrogen bond scheme was reached at a value of the β-CD/EDTA molar ratio n = 6. Finally, the connectivity pattern of “uncoupled” water molecules bound to the nanosponge backbone was found to be weakened by increasing T. The temperature above which the population of not tetracoordinated water molecules becomes predominant turned out to be independent of the parameter n.