Many natural zeolites have stronger affinity toward ammonium (NH₄⁺). In order to accommodate NH₄⁺ in it, zeolite loses its exchangeable cation. This ion-exchange property makes it a useful solution for NH₄⁺ removal from agricultural runoff. The reversibility of this ion-exchange guarantees the recovery of captured NH₄⁺ from zeolite as required, rendering it ready for further use. Alkaline hydrothermal treatment of natural zeolites improves its ion-exchange capacity. This treatment can significantly enhance their properties by incorporating extra-framework cations into their structures. These improvements are often misattributed to the original zeolite, rather than to the framework changes induced by the treatment. Alkaline hydrothermal processes can transform the structure of the parent zeolite into different types. To optimize these enhancements, chabazite (CHA), a natural zeolite, was subjected to alkaline hydrothermal treatments with different alkali concentrations, temperatures, and durations. Through an exhaustive analytical investigation including X-ray Powder Diffraction (XPD), Fourier Transform Infrared Spectroscopy (FTIR), Transmission Electron Microscopy (TEM), and 27Al and 29Si Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR), it was conclusively shown that hydrothermal treatment in an alkaline medium converted CHA into analcime (ANA), a zeolite with a denser tetrahedrally coordinated atom structure. Mesoporosity of natural zeolite, achieved through treatment, upgrades that into hierarchical zeolite. Mesopores act as an entrance for larger molecules, facilitating their movements for catalytic chemical reactions. This modification enhances the adsorption capacity of zeolite, improves mass-transfer and opens up more accessible sites in the zeolite. In this study, it has been observed that alkaline hydrothermal treatment of CHA introduced mesoporosity in the structure of modified zeolite. Alkali treatment also tailors Brønsted acidity in zeolite. Because of those Brønsted acid sites, upgraded zeolite are prone to alkalization of NH₄Cl solution of lower concentration. It has been reported by multiple researchers. However, further study to reevaluate and explain the differences of NH₄⁺ removal behavior of alkaline mediated hydrothermally treated CHA in a wider range of NH₄Cl concentration, are scarce. Treated zeolites were administered in 100-1400 mg/L of NH₄Cl solution. In this work, the parameters for the participation of Brønsted acid sites causing the alkalization of NH₄Cl solution, was briefly discussed. Because of NH₄⁺ ↔ NH₃ equilibrium is pH dependent, the proper knowledge of administering conditions of alkali mediated hydrothermally treated CHA in wastewater with NH₄⁺ in it, will reduce unnecessary complications. This modified zeolite had twice as much greater NH₄⁺ removal capacity compared to as-received natural CHA. In ion-exchange, the exchangeable univalent cations ↔ NH₄⁺ exchange occurs in equivalent ratio. However, the treated zeolite showed much higher NH₄⁺ removal with lesser Na⁺ eluted from it, in concentrated NH₄Cl solution. The role of Brønsted acid sites and mesoporous locations in that occurrence has been discussed in this report. This special property makes the upgraded zeolite suitable for NH₄⁺ shock loading. The NH₄⁺ removal capacity of treated zeolite in higher and lower NH₄Cl concentration in a fixed-bed column was examined, respectively. The material-packed bed showed excellent selectivity toward NH₄⁺ in synthetic wastewater, containing other cations. The differences of those breakthrough columns have been presented graphically. In between the column exhaustions, the loaded zeolites were regenerated with brine solution. 94 - 98 % reclamation of NH₄⁺ from exhausted zeolites into the brine solution was attained.