The nanoporous structure of collagen-glycosaminoglycan (CG) hydrogels was studied using 1H NMR spectroscopy and thermally stimulated depolarisation (TSD) current with layer-by-layer freezing-out of bulk and interfacial water. The depression of the freezing point of water is related to the size of the nanopore, to which it is confined. Changes in the Gibbs free energy of the unfrozen interfacial water are related to the amount of bound water in the hydrogel matrix and to the re-arrangement of the 3D network structure of the biopolymer. Analysis of the thermodynamic properties of bulk and interfacial water using the layer-by-layer freezing-out technique combined with NMR and TSDC provides valuable information about the structural features of CG hydrogels that can be used for characterisation of different types of hydrogels and soft tissue scaffolds, artificial skin substitutes and other biomaterials.