Ion exchange involves replacing native cations that are originally present in zeolites with other ions of the user’s choice. This method is one of the most powerful and versatile ways to improve the properties of natural zeolites and expand their functional properties for applications in various fields. Cation exchange can be implemented using various methods and produce different end results, which depend on many factors (processing conditions, duration time, pH, temperature, additional exposure to ultrasonic or microwave irradiation, etc.). In some cases, such processes can affect the zeolite structure, leading to cation migration and replacement of extra-framework elements, sometimes to leaching of the framework and altering Si/Al ratio, as well as to the creation of mesoporosity. Overall, these improved properties open up opportunities for various cost-effective applications of ion-exchanged natural zeolites in water treatment, agronomy, environmental remediation, catalysis, and others. This chapter summarizes the principles, methods, and mechanisms of ion exchange applied to natural zeolites, with an emphasis on how controlled modification expands their application in various important processes. In conclusion, the review highlights current challenges, standardization needs, and prospects for future research aimed at unlocking the full potential of ion-exchange natural zeolites.