Efforts aiming at the application of membrane-based technologies in the field of wastewater treatment have focused on tertiary treatment so as to obtain a high-quality final effluent that can be reused for different purposes. Nevertheless, while technical viability of membrane filtration is very well documented, its implementation is constrained by the high investment and operational costs involved. Numerous studies have been carried out at a pilot scale for the selection of membranes and for the optimisation of operational conditions. In this paper two membrane filtration techniques, microfiltration and ultrafiltration, applied to the secondary effluents of a conventional wastewater treatment plant, were compared. The operations within the pilot plant were evaluated, as well as the operational costs linked with them and the quality of the water output.