Background: Surface water and groundwater pollution with various forms of nitrogen such as ammonium and nitrate ions is one of the main environmental risks. The major objectives of this study were to evaluate the capacity of natural zeolite (clinoptilolite) to remove NO3- and NH4+ from polluted water under both batch and column conditions. Methods: The laboratory batch and column experiments were conducted to investigate the feasibility of clinoptilolite as the adsorbent for removal of nitrate (NO3&minus) and ammonium (NH4+) ions from aqueous solution. The effects of pH, clinoptilolite dosage, contact time, and initial metal ion concentration on NO3- and NH4+ removal were investigated in a batch system. Results: Equilibrium time for NO3 and NH4 ions exchange was 60 minutes and the optimum adsorbent dosage for their removal was 1 and 2.5 g/L, respectively. The adsorption isotherm of reaction (r> 0.9) and optimum entered concentration of ammonium and nitrate (30 and 6.5 mg/L, respectively) were in accordance with Freundlich isotherm model. The ammonium removal rate increased by 98% after increasing the contact time. Conclusion: Our findings confirm that natural Clinoptilolite can be used as one of effective, suitable, and low-costing adsorbent for removing ammonium from polluted waters.