Based on published research on modifying the structure of water and water-containing systems, we assess external influence methods: temperature, magnetic field, light radiation, and their combination. We evaluate changes in the electrophysical, photo- and pH-metric biological, therapeutic, and other properties of water systems using non-destructive electrophysical research methods, i.e., thermometry, pH, laser interference, dynamic light scattering, microelectrophoresis, conductivity, surface tension, dielectric constant, polarimetric measurements, atomic force microscopy, and UV and EPR spectroscopy. The effects of temperature or magnetic field lead to a change in the content and size of water clusters, and physicochemical, biological, therapeutic, and other changes in the properties of water and water-containing systems. The combined effect of a magnetic field and curative mud and the impact of magnetised mineral water have a more pronounced therapeutic effect than only mineral water or curative mud. The data presented indirectly indicate structural changes in water and water-containing systems. We conclude that the primary mechanism of action of a magnetic field, light, or a combination of these factors on water and water-containing systems, including mineral water and therapeutic mud, is a change in the structure of water.