The natural zeolite has been modified with sulphate and phosphate. The adsorption of thorium from the aqueous solutions by using the natural and modified zeolites has been investigated via a batch method. The adsorbent samples were characterized by X-ray Diffraction (XRD), N2 adsorption–desorption (BET), Fourier transform infrared (FTIR), field emission scanning electron microscopy (FESEM), and energy dispersive X-ray spectroscopy (EDX). Modification of natural zeolite with sulphate and phosphate was found to increase its adsorption capacity of thorium but reduced its specific surface area (SBET). The adsorption experiments were expressed by Langmuir, Freundlich and Dubinin–Radushkevitch (D–R) isotherm models and the results of adsorption demonstrated that the adsorption of thorium onto the natural and modified zeolites correlated better with the Langmuir isotherm model than with the Freundlich isotherm model. The maximum adsorption capacity (Qo) was determined using the Langmuir isotherm model at 25 °C and was found to be 17.27, 13.83, and 10.21 mg/g for phosphate-modified zeolite, sulfate-modified zeolite, and natural zeolite, respectively. The findings of this study indicate that phosphate-modified zeolite can be utilized as an effective and low-cost adsorbent material for the removal of thorium from aqueous solutions.