The high fission yield and long half life of cesium and strontium make them the two most high-risk products from nuclear fission, so their separation from radioactive wastes is an important step in mitigating their harmful effects. Clinoptilolite, because of its thermal stability, high radiation resistance, and selectivity, was considered as the adsorbent for this purpose. In order to then separate the adsorbent-adsorbate complex from aqueous solution, the clinoptilolite was prepared as a magnetized composite with nanomagnetite. This magnetically modified zeolite enabled the efficient and quick separation of the adsorbent from solution using magnetic separation. The ability of this composite to remove Cs+ and Sr2+ from aqueous solutions was assessed and characterized using X-ray diffraction, X-ray fluorescence, Fourier-transform infrared spectroscopy, differential thermogravimetric analysis, and vibrating-sample magnetometry. Variables such as initial ion concentration, pH, contact time, and temperature in the sorption process were studied and optimized. The maximum adsorption capacities of the composite were 188.7 and 36.63 mg g−1 for Cs+ and Sr2+, respectively. Investigation of the kinetics revealed that the adsorption process onto the composite was quicker than in the case of the zeolite alone. The equilibrium data were analyzed using the Langmuir, Freundlich, and Dubinin-Radushkevich (D-R) isotherm models. The mean free energy of sorption (E) for both ions was in the range 8–16 kJ mol−1, confirming that an ion-exchange mechanism had occurred. Positive ΔH∘ and negative ΔG∘ values were indicative of the endothermic and spontaneous nature of the removal of Cs+ and Sr2+. The saturation magnetization of the composite was measured (17.46 Am2/kg), implying fast magnetic separation of the sample after adsorption. The results obtained revealed that the natural Iranian zeolite nanomagnetite composite was a good ion exchanger in the removal of Cs+ and Sr2+.