It had previously been shown that ammonium selective natural zeolite clinoptilolite may be used successfully as an ion exchanger for ammonium removal and nitrogen control from domestic wastewater. The process had been reported to be acceptable either by itself alone or as an upgrade. In this work, the possibility of using clinoptilolite for ammonium removal from fertilizer production wastewater was investigated. The fertilizer plant under consideration was rather a non-typical one with a lower ammonium strength than what is normally expected, and a variable effluent concentration. Batch experiments were performed to assess the capacity of clinoptilolite towards ammonium removal from an industrial wastewater at two different pHs. Flow experiments for the characterization of system behavior under continuous feeding conditions at different contact times were conducted for breakthrough analysis. Both real and simulated fertilizer wastewater samples were investigated and the results have shown that the real one may successfully be represented by the simulated one. Experimental results have shown that surface capacities exceeding 14 mg ammonium g(-1) clinoptilolite could be attained, complete removal of ammonium may be achieved with empty bed contact times of 10 min or higher and ion exchange with clinoptilolite could be used successfully to comply with the effluent standards given for the fertilizer plant.