We reconstruct a section of the cathode catalyst layer (CCL) of a Gore PEMFC membrane electrode assembly three-dimensionally with nanometre scale resolution. Subsequently, we present a new modelling method to fill the pore space of this matrix stepwise with water, enabling the description of varying saturation conditions of the CCL. The method is based on a 3D pore size distribution and enables to differentiate between a hydrophilic and a hydrophobic CCL It utilizes a sequence to fill the pores according to their size, going from small to large (hydrophilic) or vice versa (hydrophobic), until a pre-defined value of water saturation is reached. We compare both cases by calculating an effective diffusivity for oxygen in nitrogen in all spatial directions. Both the hydrophilic and the hydrophobic case display a similar ability to transport oxygen up to approximately 50% water saturation of the pore space. At higher water saturation, we calculate larger diffusivity values for the hydrophobic case. Finally, we calculate the specific reaction surface area that is accessible from the gas diffusion layer via unfilled pores for all water saturation conditions. At 50% saturation, the hydrophobic case displays a twenty times larger reaction surface area than the hydrophilic case. (C) 2012 Elsevier B.V. All rights reserved.