Organized industrial zones (OIZs) in Turkey solve their wastewater problems by collecting and treating the wastewater using some traditional methods (mostly biological) to achieve discharge standards. However, new solutions for water reclamations are needed for the limited water sources, increasing pollution loads to the receiving environments and water basins. Membrane bioreactors (MBRs) have recently become more preferable due to their advantages over the conventional treatment methods by their decreasing investment and operational costs. In this study, the treatment performance of a submerged aerobic MBR is investigated by two different membrane materials using the influent wastewater from the primary sedimentation tank of Kayseri OIZ. For this purpose, pre-studies were done to ensure the sludge retention time (SRT), to examine membrane fouling profile, along with optimizing the flux and the hydraulic retention time (HRT). The relationships between membrane fouling and the module size were also revealed. The MBR system is fully automated with a data control system and its main operational parameters including input and output were continuously monitored. All analyses were performed according to the Standard Methods. In pre-studies, the system was continuously monitored to achieve the desired mixed liquor suspended solids (MLSS) concentrations and removal efficiencies. During this period of time, it was observed that the MLSS concentrations were increased continuously; however, this increase stopped at the low flux and the feed concentrations. So, to increase the MLSS concentration and to provide the SRT, the system must be operated at higher flux and necessary amount of the sludge calculated theoretically must be wasted. However, in this stage, the module size of the system cannot provide the flux due to clogging. As a result, this MBR system was optimized by determining the optimum membrane area, flux and SRT with the lowest membrane fouling and transmembrane pressure (TMP) increase.