Here, we model the effects of fouling on the performance of a reverse osmosis (RO) system treating micro-filtered secondary effluent. The model considers system properties, water quality, and transport phenomena. The model is fitted to operating data from the Orange County Water District's Groundwater Replenishment System RO pilot plant, which experienced severe fouling over a period of 3-4 months. Modeling results suggest the following: (a) permeate production, mass transfer, and solute rejection decrease from inlet to outlet, (b) osmotic and hydraulic pressure losses increase from inlet to outlet, (c) surface fouling by cake formation mirrors the permeate production rate (highest in lead elements, tapering off from inlet to outlet), (d) the higher fouling rate near the inlet shifts permeate production downstream, leveling the flux profile from inlet to outlet, (e) fouling-induced flux leveling leads to higher flux and rejection in tail elements, and thus, enhanced concentration polarization, (f) fouling-enhanced concentration polarization may induce premature scale formation even at fixed recovery, and (g) long-term, irreversible fouling results from combined effects of incomplete membrane cleaning and physical membrane compaction. This new model appears to be a powerful tool for understanding the behavior of full-scale RO processes. (C) 2008 Elsevier B.V. All rights reserved.