This article studies the geological structure, mineralogical composition, genesis, and sorption properties of Khonguruu zeolite deposit (Republic of Sakha, Russia). Although it is one of the largest developed deposits in Russia, detailed studies of the mineral composition and physicochemical properties have not been conducted previously, which limits its industrial potential. Zeolites were studied with X-ray diffraction (XRD), scanning electron microscopy (SEM), differential thermal analysis (DTA), X-ray fluorescence spectrometry (XRF), Fourier transform infrared spectroscopy (FTIR), Brunauer–Emmett–Teller (BET) and cation exchange capacity (CEC) analyses. Experiments on the sorption of radioactive cesium were also carried out. Zeolites formed four beds with an average content of 50–85%. The main focus of this study is on the detailed investigation of its mineral composition. These data, together with the analyses of ion-exchange complexes and color, provided an opportunity to distinguish between different types of zeolites. The zeolite minerals are represented by heulandite-1, heulandite-2 and, to a lesser extent, clinoptilolite. For the first time, a significant presence of amorphous silica was demonstrated in zeolite samples and used for correction of the crystallochemical formula of zeolites. On the basis of exchangeable cations composition, two main types of zeolites were found at the deposit: alkaline and alkaline-earth. The CEC of the zeolites ranged from 139 to 214 cmolc kg–1 and high 137Cs sorption. The zeolites have a volcanogenic-sedimentary genesis and were formed from ash material of basic and acidic composition in coastal sea waters with alternating conditions of low and high salinity. Based on the data obtained, it can be concluded that the alkaline raw material can be used as a sorbent for wastewater treatment.