Research subject. Crystals of hydrogen-containing compounds belonging to the superprotonic family. Aim. To obtain knowledge about regular relations between composition, atomic structure, real structure and physical properties of materials, with the purpose of elucidating processes occurring in condensed state and forming the basis for modification of known or obtaining new compounds. Materials and methods. Experimental data were obtained using a set of complementary physical methods, including structural analysis using X-rays, synchrotron radiation and neutrons, optical microscopy, and atomic force microscopy. Results. Experimental data on the atomic structure, real structure, and physical properties of superprotonic crystals, including systems of hydrogen bonds and their changes, were obtained. Conclusions. The physical properties of superprotonic crystals are significantly affected by hydrogen bonding systems and their changes, primarily by the formation of dynamically disordered hydrogen bonds with energetically equivalent positions of hydrogen atoms. When carrying out diagnostics of crystalline samples, account should be taken of their real structure, including the structure of surface layers and the presence of crystallization water. These factors may affect the measured physical parameters, the boundaries of existence of phases, the formation of a multiphase state under variations in temperature.