The nutrient removal performance of a membrane bioreactor (MBR) plant treating the wastewater of 10,000 PE was investigated with dynamic simulations. The average process performance with respect to chemical oxygen demand and total nitrogen were reported to be 97 and 81 %, respectively. The modeling study showed that low dissolved oxygen (DO) levels (0.2-0.3 mgO(2)/L) due to limited aeration capacity within aeration tank that provided additional total nitrogen removal of 15-20 mgN/L. Simultaneous nitrification and denitrification process was found to be the reason of performance increase. However, low DO levels < 0.3 mgO(2)/L in the aeration tank triggered the proliferation of filamentous microorganisms within one month as a side effect. In this respect, the morphotypes of Type 0092 and Nocardia (Gordonia) amarae were found to be excessively abundant in the MBR system. Overflow of foam layer covering the tanks was frequently reported during bulking period. A hypochloride dosing of 4.5 gCL/kgMLSS/day was applied to get over filamentous bulking problem as a short term action.