The effects of salinity fluctuations on the activity of autochthonous halophilic bacteria in aerobic granular sludge (AGS) and flocculent activated sludge (FAS) reactors were investigated. The response of nitrifiers and denitrifiers activity to drastic and moderate salinity shocks in the short-term (ST) and long-term (LT) was examined.The BOD5 removal efficiency decreased only in the reactors subjected to the drastic LT salinity increase. Nevertheless, stable performances were achieved 18 days after the shock in the AGS-R1 (90%), whereas after 27 days in the FAS-R1 (82%).The loss in nitritation efficiency was higher in the FAS reactors and was proportional to the shock intensity. Nitritation activity collapsed from approximately 3.8 mgNH4-N gVSS−1 h−1 to 0.73 mgNH4-N gVSS−1 h−1 and from 4.5 mgNH4-N gVSS−1 h−1 to 0.24 mgNH4-N gVSS−1 h−1 in the AGS-R1 and FAS-R1, respectively, even if the ammonium oxidation capacity did not completely disappeared. Denitritation activity decreased from 11.44 mgNO2-N gVSS−1 h−1 to 3.93 mgNO2-N gVSS−1 h−1 in the AGS-R1 at steady state, whereas in the FAS-R1, it decreased from 12.53 mgNO2-N gVSS−1 h−1 to 2.09 mgNO2-N gVSS−1 h−1.Nitritation and denitritation were completely restored 5 days after ST shock. No significant effects were observed after the moderate shock.The changes in the total EPS content were lower than 10%, therefore, it was considered negligible. Only drastic shocks caused significant changes in the EPS structure, with an increase of the loosely-bound by 45% in the AGS and 55% in the FAS.