Reverse osmosis (RO) is widely used for the production of drinking water from brackish and sea water. In RO process, pressure is used to separate water and salts by allowing water to pass through a semi-permeable membrane leaving the salts behind. Therefore, controlling membrane fouling will keep the productivity at its optimum condition. Having spacer filaments in the feed channel has proved to reduce the concentration polarization on the surfaces of the membrane and therefore fouling. In this paper computational fluid dynamics (CFD) simulations were carried out for fluid flow through rectangular channels filled with spacers. In order to (1) understand the effect of the spacers on the increase of shear stress on the membrane surface, (2) study the reduction of precipitated salt on the membrane surface and (3) monitor the mass transfer performance across the membrane surface, a computational model that includes all of the important physical processes occurring in membrane systems is required. This paper describes bespoke enhancements to a commercial CFD package, ANSYS-CFX, for modelling the selective transfer of components from the feed channel to the permeate channel through the membrane surface. To validate the new code, this work has been verified against published work and has proved to be as accurate. Further simulations were then carried out, for two different filament configurations, for channel Reynolds numbers up to 800 and with fully functioning dual-membrane channels, as found in industrial spiral-wound desalination modules for example. Results suggest that the zigzagging spacers' type is more desirable comparing with the submerged one in maintaining the membrane and desalination system performance. Crown Copyright (c) 2008 Published by Elsevier B.V. on behalf of The Institution of Chemical Engineers. All rights reserved.