The aim of this study was to test membrane modules immersed in pilot-scale domestic WWTP and in the aeration zone of the municipal WWTP Devínska Nová Ves - Bratislava. The first three phases were operated long-term without the employment of additional aeration. The fourth and fifth phases were operated with the employment of additional aeration applied as membrane cleaning in order to prevent the membrane from clogging. The operation of flat-sheet and hollow-fiber membrane modules showed similar results in permeate characteristics. Membrane modules were able to remove organic matter (as much as 92%) and more than 98% of NH₄-N in the long-term operation without activated sludge removal.