A hybrid membrane bioreactor (MBR) technology was investigated for treatment of natural waters containing natural organic matter (NOM), nitrate, alachlor and viruses. The NOM are precursors to disinfection byproducts (DBPs) such as trihalomethanes, and potential cause for microbial growth in distribution systems. Batch bioreactor studies optimized the carbon-to-nitrogen (C/N) ratio, temperature and pH for biological denitrification. Mini-pilot MBR studies with ethanol as electron donor were conducted under three scenarios: no powder activated carbon (PAC) or biomass, biomass alone, and combination of PAC and biomass. The removals of nitrate, alachlor, total organic carbon (TOC), trihalomethane formation potential (THMFP) and MS-2 virus were revaluated. Nitrite and ethanol residuals were well below their detection limits in the MBR effluent under steady-state conditions. Using biomass alone, the removal efficiencies for NOM (as TOC), alachlor, and THMFP were 60, 36 and 61%, respectively; whereas, on combining PAC and biomass they increased to 84, 99.8 and 98%. The virus rejection mechanisms postulated were size exclusion, sorption to membrane surface, attachment to bio-particles, and sorption onto foulant or cake layers. The MS-2 removals exceeded 3.8-logs under optimal process conditions. Membrane fouling and flux decline patterns under the three experimental scenarios were well described by the resistance model. The flux decline was characterized by three distinct stages, namely, initial conditioning fouling, rapid fouling, and slow fouling. The Tustin groundwater was associated with lower organic fouling but higher inorganic fouling than the Fountain Valley groundwater. (C) 2009 Elsevier B.V. All rights reserved.