This study experimented with the novel approach of using a microfiltration (MF) and reverse osmosis (RO) treatment train to treat the effluent of a primary settling tank at the Inland Empire Utility Agency in Chino, CA. The pilot used polyvinylidene fluoride hollow-fiber MF modules as pretreatment for an RO skid, which used Hydranautics ESPA2 membranes in a two-stage configuration with a feed capacity of 6 gallon per minute (gpm). In this pilot configuration, researchers monitored the removal of 38 most prevalent contaminants of emerging concerns (CECs) through the MF/RO process. To investigate how operating the RO process at two fixed recovery rates of 55% and 80% would affect the performance of the MF/RO membranes, researchers applied different fluxes (8, 10, 12 and 14 gal/d/ft2 (gfd)) and evaluated the removal of CECs in 1-stage and 2-stage RO configurations. The occurrence of CECs in the MF influent, MF effluent, RO permeate, and RO concentrate were analyzed and studied. In the first phase (1-stage the RO process), flux of 14 gfd showed a better rejection value of inorganics (95.2%) when compared with those of other fluxes. Meanwhile, in the second phase (2-stage RO process), flux of 12 gfd showed a better rejection of inorganics (93.7%) when compared with those of other fluxes. Although concentrations of CECs slightly decreased in the RO permeate as the flux has increased, statistical analysis showed no significant differences between different fluxes in terms of CEC rejection.