The current study aims to highlight the effect of flow pattern on the variations of permeate fluxes over the membrane surface during desalination in a direct contact membrane distillation (DCMD) flat module. To do so, a three dimensional (3D) Computational Fluid Dynamics (CFD) model with embedded pore scale calculations is implemented to predict flow, heat and mass transfer in the DCMD module. Model validation is carried out in terms of average permeate fluxes with experimental data of seawater desalination using two commercially available PTFE membranes. Average permeate fluxes agree within 6% and less with experimental values without fitting parameters. Simulation results show that the distribution of permeate fluxes and seawater salinity over the membrane surface are strongly dependent on momentum and heat transport and that temperature and concentration polarization follow closely the flow distribution. The analysis reveals a drastic effect of recirculation loops and dead zones on module performance and recommendations to improve MD flat module design are drawn consequently.