Membrane Bioreactor (MBR) being the promising and sustainable technology, will be highly in demand in future. To monitor the inline status of fouling, in order to make the process more economical, novel fouling monitoring indexes based on the differences in filtration properties between the filtration direction and backwashing direction were developed. The module clogging and fouling properties were monitored by direct visual observation of filtration surface, filtration resistance and zeta potential for both directions in a lab scale MBR using alumina tubular microfiltration membrane having pore size of 0.2 μm. The optimal clearance size of flow channel in membrane module for avoiding clogging by sludge cake was determined at 5 mm by the visual observation. The filtration resistance for filtration direction, RF, increased steeply in later stage of operation while that for backwashing direction, RB, showed a gradual increasing throughout operation. This difference between RF and RB was elucidated by a model where the sludge cake behaves like a “check valve”. The analysis of cleaning experiments of fouled membrane with the resistance in series model also supported the model of the sludge cake behavior and showed that the resistance caused by sludge cake, Rcake, dominated RF and had no impact on RB. This analysis also showed that Rcake and the resistance caused by macromolecule adsorption, Radsorption, which are important factors for recognizing fouling status, can be evaluated from RF and RB, which are easy to monitor during operation, without cleaning experiments. The zeta potential also depended on the measurement direction and showed a decreasing trend with the increase in filtration resistance.