In this work, we present a novel methodology for incorporating the effect of fibre surface morphology on liquid water transport in polymer electrolyte membrane fuel cell gas diffusion layers (GDLs). Roughness features presented on the surface of the fibre are analysed using atomic force microscopy and are found to significantly impact the capillary pressure of liquid water pathways propagating through the GDL. A threshold capillary pressure was defined as the largest capillary pressure exhibited by the liquid water phase during the invasion of the throat. The threshold capillary pressures observed in the presence of roughness features are significantly greater than those in the absence of roughness features. Two-dimensional circumferential roughness models in cylindrical and converging-diverging throats are established, and an interfacial meniscus advancing algorithm is presented to determine the resulting threshold capillary pressures required for liquid water penetration. Revised Young-Laplace equations, which are particularly useful for pore network modeling, are suggested for calculating threshold capillary pressures that account for the effect of the roughness of throats with intrinsic contact angles greater than 90 degrees.