This study utilises computational fluid dynamics simulations with the OpenFOAM computational framework to investigate and compare the in-plane and through-plane permeability properties of four different gas diffusion layers (GDLs). Also the through-plane water and air relative permeability values and water saturations at different rates were simulated. Permeability analysis enhances our understanding of fluid flow, ways to decrease pressure loss in the GDL, and methods to enhance oxygen concentration at the catalyst layer interface through convection. The analysis reveals that the investigated GDL materials have spatial heterogeneity of porosity and permeability, especially in the Sigracet SGL 25 BA GDL. However, the porosity and permeability of the Toray TGP-H 060 and AvCarb 370 MGL GDLs exhibit less variations. The two-phase flow studies on GDL saturation show that at the same water injection flowrate, the AvCarb 370 MGL GDL has the largest remaining water saturation, with Sigracet SGL 25 BA GDL being the less saturated GDL among the four investigated GDLs. The compression from the ribs significantly affected the in-plane permeabilities of both Toray TGP-H 060 and especially impacted Sigracet SGL 25 BA GDL. This impact was expected as the pore size distribution varied significantly in the areas under the ribs versus the channel.