This research investigated the integrity of reverse osmosis (RO) and nanofiltration (NF) membrane systems with respect to microbial passage using microbial (bacteriophage MS2 viruses) and nonmicrobial (Rhodamine WT [RWT] dye and fluorescent-dyed polyslyrene microspheres) surrogates. Pilot-scale experiments were conducted with microfiltered secondary wastewater effluent and conventional process-treated surface water. Microspheres were a more accurate predictor of MS2 removal; however, RWT showed good correlation, particularly for RO. NF and RO elements compromised via a membrane pinhole showed reduced removals for all surrogates, whereas subsequent operation of such elements increased surrogate removal (through membrane fouling). This increase was reversible by chemical cleaning for element; operated on effluent but less so for surface water. Compromising RO system integrity using cut O-rings did not increase surrogate passage. Passage increased only when sections of the O-rings were removed. The impact on integrity of such an O-ring compromise was dependent on location in the RO/NF system.