Adding a hydrophobic micro-porous layer (MPL) between a gas diffusion layer (GDL) and a catalyst layer (CL) at the cathode of a PEM fuel cell was found capable of improving cell performance. However, how an MPL does this is not well-understood because current techniques are limited in measuring, observing and simulating multiphase pore fluid flow across the full range of pores that vary to a great extent in geometry, topology, surface morphology. In this work, we focused our investigation on estimating flow properties of an MPL volume to assess the limiting effect of strongly hydrophobic sub-micron pores on water transports. We adopted a nano-tomography and pore network flow modelling approach. A pore-structure model, purposely reconstructed from an intact MPL sample using Focused Ion Beam milling and Scanning Electron Microscope (FIB/SEM) previously, was used to extract a realistic pore network. A two-phase pore network flow model, developed recently for simulating the flow of gas, liquid or their mixture in both micrometre and nanometre pores, was applied to the pore network. We firstly tested the validity of the constructed pore network, and then calculated the properties: permeability for both water and selected gases, water entry pressure, and relative permeability. Knudsen diffusion was taken into consideration in calculations when appropriate. Our calculations showed that the water permeability was three orders of magnitude smaller than experimentally measured results reported in the literature, and when the water contact angle increased from 95 degrees to 150 degrees, the water-entry pressure increased from 2.5 MPa to 28 MPa. Thus our results revealed that for a strongly hydrophobic MPL that contains nanometre pores only it would behave like a buffer to water, and therefore the structural preferential paths in an MPL, such as cracks, are likely to be responsible for significant liquid water transport from the CL to the GDL that has been observed experimentally recently. We highlighted the needs for multi-scale modelling of the interplays of liquid water and gas transfer in MPLs that contain variable pores. (C) 2014 Elsevier Ltd. All rights reserved.