The effects of microfiltration (MF) as pretreatment for reverse osmosis (RO) on biofouling of RO membranes were analyzed with secondary wastewater effluents. MF pretreatment reduced permeate flux decline two- to three-fold, while increasing salt rejection. Additionally, the oxygen uptake rate (OUR) in the biofouling layer of the RO membrane was higher for an RO system that received pretreated secondary wastewater effluent compared to a control RO system that received untreated secondary effluent, likely due to the removal of inert particulate/colloidal matter during MF. A higher cell viability in the RO biofilm was observed close to the membrane surface irrespective of pretreatment, which is consistent with the biofilm-enhanced concentration polarization effect. Bacterial 16S rRNA gene clone library analysis revealed dominant biofilm communities of Proteobacteria and Bacteroidetes under all conditions. The Cramer-von Mises test statistic showed that MF pretreatment did not significantly change the bacterial community structure of RO membrane biofilms, though it affected bacterial community structure of non-membrane-associated biofilms (collected from the feed tank wall). The finding that the biofilm community developed on the RO membrane was not influenced by MF pretreatment may imply that RO membranes select for a conserved biofilm community.