A two-dimensional two-phase non-isothermal mass transport model is developed to numerically investigate the behavior of water transport through the membrane electrode assembly (MEA) of a direct methanol fuel cell. The model enables the visualization of the distribution of the liquid saturation through the MEA and the analysis of the distinct effects of the three water transport mechanisms: diffusion, convection and electro-osmotic drag, on the water-crossover flux through the membrane. A parametric study is then performed to examine the effects of the structure design of the gas diffusion layer (GDL) on water crossover. The results indicate that the flow-channel rib coverage on the GDL surface and the deformation of the GDL can cause an uneven distribution of the water-crossover flux along the in-plane direction, especially at higher current densities. It is also found that both the contact angle and the permeability of the cathode GDL can significantly influence the water-crossover flux. The water-crossover flux can be reduced by improving the hydrophobicity of the cathode GDL. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.