Natural zeolites are mainly framework silicates with large open cavities occupied by cations and water molecules. These minerals are abundant all over the world and applied as ion exchangers for large scale remediation (e.g. radionuclides extraction from contaminated soils in Chernobyl and Fukushima). We study the extra-framework cation arrangement of natural zeolites under different environmental conditions (temperature and humidity) by single crystal X-ray diffraction methods to understand the bonding between framework and cavity occupants and its influence on framework distortions. This basic research approach has strong bearing on application of zeolites in chemical technology and environmental remediation.