Topologically equivalent pore network modelling of polymer electrolyte membrane (PEM) fuel cell gas diffusion layer (GDL) materials was employed to simulate ex-situ liquid water invasion experiments commonly conducted to investigate multiphase transport in PEM fuel cells. Stochastic, three dimensional pore spaces are numerically reconstructed to mimic carbon fibre paper based GDL materials. A watershed based method was used for extracting pore networks from a range of sample sizes. Invasion percolation was employed to simulate liquid water originating at one surface of the material and percolating through to the opposite surface. Inlet reservoir areas were chosen to mimic those used in ex-situ experiments in literature. It was found that sample size has a strong overall effect on saturation levels and inlet conditions primarily affected saturation near the inlet.