A three-dimensional, multicomponent, two-fluid model developed in the commercial CFD package CFX 13 (ANSYS Inc.) is used to investigate the effect of porous media compression on water transport in a proton exchange membrane fuel cell (PEMFC). The PEMFC model only consist of the cathode channel, gas diffusion layer, microporous layer, and catalyst layer, excluding the membrane and anode. In the porous media liquid water transport is described by the capillary pressure gradient, momentum loss via the Darcy-Forchheimer equation, and mass transfer between phases by a nonequilibrium phase change model. Furthermore, the presence of irreducible liquid water is taken into account. In order to account for compression, porous media morphology variations are specified based on the gas diffusion layer (GDL) through-plane strain and intrusion which are stated as a function of compression. These morphology variations affect gas and liquid water transport, and hence liquid water distribution and the risk of blocking active sites. Hence, water transport is studied under GDL compression in order to investigate the qualitative effects. Two simulation cases are compared; one with and one without compression.