Abstract Microcoagulation has recently been considered as a promising pretreatment for an ultrafiltration (UF) process from numerous studies. To investigate the effects of microcoagulation on the performance of the UF–reverse osmosis (RO) system treating wastewater with high and fluctuant salinity, different dosages of coagulant (poly-aluminum chloride) were added prior to the UF unit in a pilot-scale UF–RO system for a 10-week period operation. Microcoagulation obviously improved the contaminant removal and cleaning efficiencies, including water backwash, chemical enhanced backwash and cleaning in place processes. Organic fouling was dominated during the initial stage of the RO membrane fouling. The microbial communities of water samples and foulant on the RO membrane were similar to those of seawater and foulant on the RO membranes from seawater RO plants. The microbial community of the foulant on the membrane was similar to that of UF permeate and RO concentrate. These results demonstrated that microcoagulation could improve the performance of the UF–RO system treating the effluent with high and fluctuant salinity from a coastal municipal wastewater treatment plant.