The concentrate streams generated from reverse osmosis (RO)-based municipal wastewater reclamation processes contain organic substances and nutrients at elevated concentrations, posing environmental and health risks on their disposal to confined receiving environments such as bays. The impact of salinity (TDS at 7, 10 and 16 g/L) of a RO concentrate (ROC) on the treatment efficiency of a biological activated carbon (BAC) system after pre-oxidation with UV/H2O2 was characterised in terms of removal of organic matter and nitrogen species, and the bacterial communities. Organic matter removal was comparable for the ROC over the tested salinity range, with 45–49% of DOC and 70–74% of UVA254 removed by the combined treatment. However, removal in total nitrogen (TN) was considerably higher for the ROC at the high salinity (TDS ∼ 16 mg/L) compared with the low (∼7 g/L) and medium salinity (∼10 g/L). Effective nitrification with high ammonium removal (>90%) was achieved at all salinity levels, whereas greater denitrification (39%) was obtained at high salinity than low (23%) and medium salinity (27%) which might suggest that the bacterial communities contributing to the greater denitrification were more halotolerant. Microbiological characterisation using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and culture based techniques showed that diversified bacterial communities were present in the BAC system as evident from different 16S rDNA. The major bacterial groups residing on the BAC media belonged to Bacillus (Firmicutes), Pseudomonas (γ-Proteobacteria), and Rhodococcus (Actinobacteria) for all salinity levels, confirming that these microbial communities could be responsible for carbon and nitrogen removal at the different salinity levels. This has implications in understanding the effectiveness and robustness of the BAC system over the salinity range of the ROC and so would be useful for optimising the treatment efficiency of the BAC system.