Abstract In this study, a multi-phase, two-dimensional model that integrates the bipolar plate (BP) and gas diffusion layer (GDL) interfacial morphology was developed to understand the effects of this interface on mass, charge and heat transport and performance of polymer electrolyte fuel cells (PEFCs). Two different case studies were performed. The first case assumes a perfect contact interface between the BP and GDL, whereas in the second case, the BP|GDL interfacial layer was incorporated as a separate domain based on the measured BP|GDL morphology. In the BP|GDL interface case, the interfacial voids were assumed to be filled with liquid water to investigate the role of the interfacial voids. For both cases, the effects of different current densities on the in-plane temperature, saturation, and oxygen concentration distribution in the GDL were investigated. Simulations indicate that the Ohmic and concentration losses are increased due to the inclusion of the realistic BP|GDL interface. The electrical contact resistance contribution of the BP|GDL interface was predicted to be 3.8 mΩcm 2 . The saturation in the GDL was found to be higher for the BP|GDL interface case, which results in higher concentration losses. The temperature was predicted to be slightly higher for the BP|GDL interface case, which could be attributed to the higher thermal contact resistance due to the fewer contact regions at the interface.