In order to achieve an efficient and economical advanced drinking water treatment system, relationships between some operational conditions, membrane filtration flux and water qualities were examined by using pilot plant, including unit processes of ozonation, ozone resistant microfiltration (MF) module and granular activated carbon (GAC) tower. From the experimental results, it became obvious that it was necessary to keep residual ozone concentration of more than 0.3mg/L on the membrane surface in order to obtain a high membrane filtration flux. The long term running test was carried out at the flux of 5m^3/m^2/day in the condition of maintaining residual ozone concentration of 1mg/L on the membrane surface with ozone dosage of 2 to 6mg/L. Moreover, quality of the produced water from GAC tower constantly satisfied the Japanese drinking water standard, and removal ratio of odor-causing substances such as 2-MIB and geosmin was more than 99%.