A novel method for efficiently removing low levels of ammonium contamination from the aqueous solution using clinoptilolite in a high-gravity rotating packed bed (HGRPB) was developed. Our batch experiments have shown that irregular clinoptilolite gave better ammonium removal efficiencies due to higher specific surface area, and the adsorption data fitted better using pseudo-second-order adsorption kinetics than pseudo-first-order adsorption kinetics. HGRPB experiments have demonstrated that increasing rotating speeds will improve ammonium removal due to higher mass transfer of ammonium between the liquid and solid phases. The removal efficiency was 90% at the end of the fifth cycle (～54 min) at a rotating speed of 1500 rpm using irregular clinoptilolite, with an initial ammonium concentration of 12.5 mg-N/L in distilled water and a flow rate of 180 mL/min. However, the removal efficiency was obviously lower in pond water than that in distilled water because of possible competitive adsorption of other cations in the pond water, suggesting modification of clinoptilolite to increase its selectivity for ammonium will be critical. This study has demonstrated the potential of using clinoptilolite in the HGRPB system to remove low levels of ammonium contamination in water and warrants the research need of HGRPB for biphasic liquid–solid adsorption processes.