Two pilot plant systems were investigated for the treatment of wastewater subject to a gradual increase of salinity. In particular, a membrane bioreactor (MBR) and a moving bed biofilm membrane bioreactor (MB-MBR) were analyzed. Carbon and ammonium removal, kinetic constants and membranes fouling rates have been assessed. Both plants showed very high efficiency in terms of carbon and ammonium removal and the gradual salinity increase led to a good acclimation of the biomass, as confirmed by the respirometric tests. Significant biofilm detachments from carriers were experienced, which contributed to increase the irreversible superficial cake deposition. However, this aspect prevented the pore fouling tendency in the membrane module of MB-MBR system. On the contrary, the MBR pilot, even showing a lower irreversible cake deposition, was characterized by a higher pore fouling tendency.