A numerical framework is developed for simulating pore-scale liquid water transport in polymer electrolyte fuel cell (PEFC) diffusion media (DM) as measured by X-ray computed tomography. Accuracy of the model is evaluated by benchmarking it with micro-scale tomographic observations of liquid water in DM at different inlet pressures. Application of the model to nano-scale morphology of the micro porous layer (MPL) shows that cracks in MPL facilitate water management by keeping nano-pores dry. Simulations in macro-scale morphology of DM indicate that liquid water saturation is approximately two-times higher in DM without an MPL. This is shown to be a consequence of water accumulation in the middle-lower height of the DM in the absence of an MPL which is demonstrated to limit the water intrusion into DM. Simulation of the land-channel configuration shows water accumulation predominantly under the land of DM with an MPL whereas considerable amount of water is also observed under the channel without an MPL. Additionally, we performed direct reactant transport simulations showing that MPL facilitates significantly better O-2 transport in wet DM (similar to two-times higher formation factor in land-channel configuration) but it induces slightly less facile O-2 transport in dry DM (12% lower formation factor). (C) The Author(s) 2019. Published by ECS.