Computational fluid dynamic simulations were conducted to investigate the effects of the membrane properties and operational parameters on the system performance in three-dimensional direct contact membrane distillation modules. The membrane thickness, porosity, pore size, feed flow rate, and the inlet feed temperature were considered in the parametric study. Water flux, temperature and concentration polarization characteristics of the membrane were determined. The net-type spacers were used in the feed and permeate channel to mitigate the polarization and enhance the flux performance of the separation module for various flow rates. The laminar model was employed to characterize the velocity, temperature and concentration field in the empty channels and the k-ω shear stress turbulence model was employed in the module containing spacers. The permeation flux, intensity of temperature and concentration polarization increase as the thickness is reduced, and the porosity and the pore size are increased. The rate of permeation and polarizations are increased with increase in flow rate. The presence spacers enhance the membrane flux performance more than 50% and mitigate polarizations up to 30%.