This paper presents a numerical simulation method for reasonably describing concentration polarization in a spacer-filled channel of a spiral-wound reverse osmosis membrane module. The permeation across the membrane was modeled theoretically, based on nonequilibrium thermodynamics. We then simulated flow and mass transfer in a periodic unit model of the spacer-filled channel, with different Reynolds numbers, spacer separations, and angles between spacers, using the proposed method as a boundary condition for the reverse osmosis membrane. The results show that the concentration polarization and water flux distribution on the membrane surface can be reasonably well expressed by the simulation. The present numerical method is effective for modeling concentration polarization, and provides better descriptions of the flow and mass transfer characteristics in the spacer-filled channel than previous simulation methods.