In this study, we investigated the possibility of auto control and the proper operating factors in the BNR(Biological Nutrient Removal) process using an NADH(Reduced Nicotinamide Adenine Dinucleotide) fluorometer, which characterized the emitted fluorescence when activated by flashes of UV light at 460 nm. In terms of finding adequate operating parameters, results indicted that nitrification efficiency decreased in the controlled DO while denitrification efficiency decreased in the controlled pH. The above results indicated that controlled operating condition after combination with NADH, DO and pH was resonable. Result obtained from the correlation between NADH and pH showed that variation trend of influent loading was similar to those of NADH and pH, and also the variation cycle was repeated on a daily basis. Consequently, this result showed the increase of BOD loading caused the nitrification efficiency to decrease because air-flow, required for nitrification, was reduced, and so the NADH value was increased. From these results, it is possible to use NADH flourimetry to assess the variation of organic load and nitrification efficiency in the case of small change in influent pH such as in sewage and also to handle and operate the load variation in the auto control system using the NADH fluorometer.