Modeling and simulation of membrane-based solvent extraction is conducted by computational fluid dynamics (CFD). The process is used for removal of priority organic pollutants from aqueous waste streams in nanoporous membranes. The pollutants include phenol, nitrobenzene, and acrylonitrile extracted by organic solvents. The mathematical model commonly applied to predict the performance of membrane-based solvent extraction is the conventional resistance-in-series model. Here, a comprehensive mathematical model is developed to predict the transport of pollutants through nanoporous media. In order to predict the performance of the separation process, conservation equations for pollutants in the membrane module are derived and solved numerically. The model is then validated through comparing with experimental data reported in the literature. The simulation results were in good agreement with the experimental data for different values of feed flow rates.