In the present study, the effect of short-term salt shocks (13% and 20%) on the performance of a halophilic MBR bioreactor used to treat a hypersaline (5% salt) synthetic wastewater was considered. 13% and 20% salt shocks resulted in a transient and permanent decrease in chemical oxygen demand removal efficiency, respectively which could be correlated with soluble microbial products (SMP) concentration and specific oxygen uptake rate values of the halophilic population. DNA leakage tests suggested that both 13% and 20% short-term salt shocks resulted in some cell structural damage. During both 13% and 20% salt shocks mixed liquor SMP, extracellular polymeric substances (EPS), zeta potential and endogenous respiration increased while relative hydrophobicity, EPSp/EPSc and exogenous respiration decreased; in both cases, however, the pre-shock values for these parameters were restored after the removal of the salt shock. 13% salt shock resulted in a transient increase in the membrane fouling rate and a permanent rise in total membrane resistance (Rt). On the other hand, both membrane fouling rate and Rt increased during 20% salt shock. Membrane fouling rate initially reduced after the 20% salt shock removal but after 5 days a “TMP jump” occurred. The latter was caused by the higher steady state SMPc and SMPp concentrations after removal of 20% salt shock compared to pre-shock values. This might have either resulted in a decrease in critical flux or an increase in local flux above critical flux in some parts of the membrane. The contribution of cake layer resistance to overall membrane resistance increased after the 13% and 20% salt shocks. The findings of the present study reveal the robustness of halophilic MBRs against salt shocks in the treatment of hypersaline wastewater. However, in cases of very high salt shocks, appropriate membrane fouling reduction strategies should be carried out during its operation.