In this study, a three-dimensional numerical model, based on the volume-of-fluid (VOF) method, was developed to investigate the water transport characteristics in the cathode of a proton exchange membrane fuel cell (PEMFC) taking into account the deformation of the gas diffusion layer (GDL). Simulations are carried out with different inlet flow rates, amount of liquid water in the GDL, positions of water droplet in the flow channel, and contact angles of the GDL and flow channel surfaces. Two mechanisms of liquid water droplet leaving the GDL are observed. One is driven by the surface tension when the gas flow rate is low, whereas the other is driven by the gas flow at high gas flow rates. Meanwhile, the deformation of the GDL and other factors highly influence the water droplet dynamics.