A membrane bioreactor (MBR) and a hybrid moving bed biofilm reactor-membrane bioreactor (hybrid MBBR-MBR) for municipal wastewater treatment were studied to determine the effect of salinity on nitrogen removal and autotrophic kinetics. The biological systems were analyzed during the start-up phase with a hydraulic retention time (HRT) of 6 h, total biomass concentration of 2,500 mg L-1 in the steady state, and electric conductivities of 1.05 mS cm-1 for MBR and hybrid MBBR-MBR working under regular salinity and conductivity variations of 1.2-6.5 mS cm-1 for MBR and hybrid MBBR-MBR operating at variable salinity. The variable salinity affected the autotrophic biomass, which caused a reduction of the nitrogen degradation rate, an increase of time to remove ammonium from municipal wastewater and longer duration of the start-up phase for the MBR and hybrid MBBR-MBR.