Computational fluid dynamic (CFD) technique was used to model a counter-currently flat-sheet membrane desalination (MD) seawater purification system. The model was implemented to reveal what features and working circumstances could be altered to optimize the seawater purification process. A 2D mathematical model was presented to explain seawater purification using direct contact membrane desalination (DCMD) system. The proposed model was based on coupling the conservation equations for water molecules in three domains of the contactor module and finite element method (FEM) method was used to solve governing equations. The model takes into account the radial and axial diffusivity of water molecules as well as thermal conductivity in the pores of the contactor. It also considers convection in heat and mass transfer in hot and cold channels. CFD method was employed for coupling equations involving heat, mass and momentum equations. The model was validated with experimental data and excellent agreement was found between experimental data and model prediction. The experimental data and current simulation revealed that with enhancing channel length, temperature of concentrated stream, and ε/τ·δ ratio or reducing the inlet velocity of concentrated solution, the salt rejection could be enhanced. The model findings have also ascertained that restrictions exist in the optimization of seawater purification system. Any variation in operating conditions or process characteristics that occurred during seawater desalination has the potential to change other process performance and might eventually affect worse process characteristics. The simulation and experimental results confirmed that the contactor module was very efficient in seawater purification.