The removal of ammonia from wastewaters after secondary biological treatment can successfully be achieved by ion exchange. However, the presence of residual organic compounds can impart significant influence on the uptake and their presence may need to be considered during the design of a treatment system. The aim of this work was to determine the effect of the presence of certain organic compounds upon the uptake of ammonium ion and column breakthrough. Two organic contaminants were considered, including citric acid and protein (as whey protein isolate). Three cationic exchangers were used and included the natural zeolite clinoptilolite, the gel resin Dowex 50w-x8, and a macronet resin, Purolite MN-500. The influence of regeneration upon column breakthrough behaviour was also determined. The results showed that the presence of organic compounds had variable effects on ammonium ion uptake. In the case of clinoptilolite the presence of protein appeared to have very little effect upon breakthrough capacity. In the case of the clinoptilolite and the MN500 a substantial reduction of breakthrough capacity was observed in the presence of citric acid. In the case of clinoptilolite a very significant increase in column breakthrough performance was observed after cycles of exhaustion and regeneration. This was not observed in the case of the synthetic resins, which showed a more consistent performance from run to run. Overall the Dowex50w-x8 gave the highest breakthrough capacity for ammonium ion removal of 700 bed volumes. Regenerated clinoptilolite showed a maximum breakthrough capacity of 450 bed volumes, and MN-500 a consistent breakthrough capacity of 300 bed volumes. (c) 2006 Society of Chemical Industry.