In this work, a lab-scale submerged OMBR system was developed and operated using synthetic wastewater for 108 days. Significant salt accumulation was observed in the OMBR, which led to a negative effect on system performance, in particular NH4-N removal (which accumulated to around 10.0 mg/L within the bioreactor), and resulted in a major shift in the bacterial community structure. A rapid recovery of pollutant removal efficiencies was achieved as NH4-N in the bioreactor decreased to around 2.0 mg/L and the microbial community acclimatized to the elevated saline environment. The average overall NH4-N and TOC removal efficiencies after restoration were 98.3% and 98.6% with NH4-N and TOC in the DS lower than 1.0 and 5.0 mg/L, respectively.