Suspended and waterborne polyurethane immobilized nitrifying bacteria have been adopted for evaluating the effects of environmental changes, such as temperature, dissolved oxygen (DO) concentration and pH, on nitrification characteristics under conditions of low ammonia concentrations. The results showed that nitrification was prone to complete with increasing pH, DO and temperature.Sensitivity analysis demonstrated the effects of temperature and pH on nitrification feature of suspended bacteria were slightly greater than those of immobilized nitrifying bacteria. Immobilized cells could achieve complete nitrification at low ammonia concentrations when DO was sufficient. Continuous experiments were carried out to discuss the removal of ammonia nitrogen from synthetic micropollute source water with the ammonia concentration of about 1 mg/L using immobilized nitrifying bacteria pellets in an up-flow inner circulation reactor under different hydraulic retention times (HRT). The continuous removal rate remains above 80% even under HRT 30 min. The results verified that the waterborne polyurethane immobilized nitrifying bacteria pellets had great potential applications for micro-pollution source water treatment.