The membrane bioreactor (MBR) integrates well within the conventionally activated sludge system regarding advanced membrane separation for wastewater treatment. Over the last decade, a number of MBR systems have been constructed worldwide and this system is now accepted as a technology of choice for wastewater treatment especially for municipal wastewater. The aim of this work was to investigate and compare submerged MBR with conventionally-activated sludge system for the treatment of municipal wastewater in Maribor, Slovenia. It can be concluded from the results, that the efficiencies being determined by the parameters were satisfied, such as, chemical oxygen demand, total phosphorous, and total nitrogen, which were 97%, 75%, and 90%, respectively. The efficiencies of ultrafiltration membrane for the same parameters were also determined, and compared with biological treatment. The results of this analysis show an additional effect regarding an improvement in the quality of the permeate but primary treatment is also very important. For successfully application of MBR system smaller grid for primary treatment is needed.