A two-dimensional comprehensive model was developed to predict the transport of water in the nanoporous membrane contactors. The considered membrane distillation device was a counter-current flat-sheet membrane contactor for production of pure water from saline water. The developed model formulates the fundamental transport equations of heat, mass, and momentum in the membrane contactor. The computational fluid dynamics techniques were applied for numerical simulation of model equations. The simulation results were compared with experimental data obtained from literature and showed great agreement with the measured values. A combination of the Knudsen flow and Poiseuille flow was used in the model for estimation of diffusion inside the membrane pores and increased the accuracy of the model. Simulation results revealed that, in the regions adjacent to the membrane wall, the temperature difference is significant. This could be attributed to the fact that a temperature boundary layer is formed near the membrane wall and causes a high temperature decline in this region.