Clinoptilolite is a natural microporous material possessing a versatile range of cation exchange properties that are exploited in many industrial processes. The dehydration and cation mobility of three prototype forms, Cs-, K-, and Na-clinoptilolite, have been studied using in situ synchrotron energy dispersive and microcrystal diffraction with a novel hybrid simulation technique. This exposes the different responses of the framework, cation, and water components to dehydration processes. The responses are illustrated for the Cs and Na forms using structural snapshots and statistically averaged parameters. The "heat collapse" framework transformation has been identified with the pure Na form by both the in situ diffraction data and the computer modeling.