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Disinfectant-containing wastewaters have been generated from many places, including marine industries. The synthetic NaClO-containing wastewaters have been effectively treated in a saline MBBR-MBR (moving bed biofilm reactor & membrane bioreactor) system containing marine microorganisms. A low concentration of NaCl (below 100 mg/L) is not enough to kill the microorganisms, but can affect their bioactivity and induce membrane biofouling. A linear relationship has been obtained for the half-life of membrane biofouling as a function of the NaClO concentration (10–100 mg/L): [half-life] = 25–0.12 × [NaClO concentration]. The COD and NH3–N removals are the highest at a salinity of 30 g/L for the marine bioreactors. The behaviour of the typical biofoulants, measured real-timely by fluorescence spectroscopy, can indicate the levels of membrane biofouling and microbial activity, responding to the NaClO and NaCl influences. Based on the behaviour of biofoulants, this work has also proposed a novel strategy of biofoulants monitoring for membrane antifouling, where antifouling responses can be carried out when the concentration of biofoulants significantly increases., Graphical abstract Image 1, Highlights • The NaClO-containing wastewaters were treated in a saline MBBR-MBR system. • The synergistic toxicity from NaClO and NaCl was observed to the microorganisms. • The behaviour of biofoulants showed the levels of fouling and biodegradability. • A novel strategy of biofoulants monitoring was proposed for membrane antifouling.