This study presents a complete three-dimensional, two-phase transport model for proton exchange membrane fuel cells based on the two-fluid method, which couples the mass, momentum, species, and electrical potential equations. The different liquid water transport mechanisms in the flow channels, gas diffusion layers, catalyst layers, and membrane are modeled using two different liquid water transport equations. In the flow channels, gas diffusion layers, and catalyst layers, the generalized Richards equation is used to describe the liquid water transport including the effect of the pressure gradient, capillary diffusion, evaporation and condensation, and electro-osmotic, while in the membrane, the liquid water transport equation only takes into account the effect of back diffusion and electro-osmotic. Springer’s model is utilized on the catalyst layer-membrane interface to maintain continuum of the liquid water distribution. The model is used to investigate the effect of flow channel aspect ratio on the performance of fuel cells with single and triple serpentine flow fields. The predictions show that for both flow fields, the cell performance improves with decreasing aspect ratio. The aspect ratio has less effect on the cell performance for the triple serpentine flow field than for the single serpentine flow field due to the weaker under-rib convection.