The authors have proposed a novel biofilm-membrane reactor (BMR) in which nitrifying biofilm is fixed on the surface of the rotating membrane disk. With this reactor, both strict solid-liquid separation and oxidation of ammonia nitrogen can be simultaneously performed. Based on the knowledge obtained in the previous experiments with the bench-scale equipment, a pilot scale study was conducted using river water at a water purification plant. The results obtained in the pilot study can be summarized as follows: (1) A pilot scale BMR worked successfully even with the water from an actual drinking water source. By implementation of pre-treatment (coagulation and sedimentation), the filter run could be continued for more than 8 months without any chemical washing. (2) The sponge cleaning developed in this study was found to be very effective. This indicates that the accumulated cake resistance is dominant in the practical situation. (3) Sufficient nitrification was observed when water temperature was high. (4) In addition to the nitrification, biological oxidation of AOC and manganese can be expected with the BMR. In this study, both AOC and manganese concentration in the permeate decreased to a level less than 10 μg/L.