The ion selective microelectrodes (ISME) have been applied to observe the continuous profiles of NO3-N and NH4-N in bulk solutions or biofilms. In order to evaluate the performance and applicability of ion concentration measuring system, the characteristics, such as slope of calibration curve, detection limit and potentiometric selectivity coefficient were investigated. The slopes of calibration curve showed high degree of correspondence for each target ion concentrations. And the detection limits of nitrate and ammonia ion selective microelectrode were 10-4.7 M and 10-4.4 M, respectively. These ion selective microelectrodes were proved that their own performance could be maintained for 16 days after making. NO3-N and NH4-N selective microelectrodes were also adapted to detect the continuous ion profiles of cilia media packed MLE (Modified Ludzack-Ettinger) process. And the monitored nitrate and ammonia ion profiles with the ion selective microelectrode were stable and well corresponded to the results with conventional ion chromatograph. However, the electric potential was unstable until 8 hr because of the unknown noise. The tip shape and performance of the ion selective microelectrode was stably kept over 2 days continuous monitoring.