The water in a proton exchange membrane water electrolyzer (PEMWE) used for hydrogen production undergoes a multiphase flow, which makes it difficult to analyze the mass transfer phenomenon and predict the performance of the PEMWE. Therefore, the multiphase flow in the PEMWE requires a comprehensive study. This work theoretically investigates multiphase mass transfer along with the electrochemical reaction in a PEMWE using a three-dimensional computational modeling approach. First, the model was validated based on an in-house experiment, and a good agreement was achieved. Subsequently, the spatial distribution of species and the electrochemical process were investigated, and the liquid water saturation level was monitored. It was observed that the high current density results in low liquid saturation in the cathode. Oxygen is accumulated under the land owing to its longer diffusion path. Higher temperatures increase and decrease liquid saturation in the cathode and anode, respectively, because they weaken the capillary transport of water inside the porous layer. The concentration overpotential is significantly lower than the activation overpotential. Furthermore, it was found that the high porosity and low contact angle of the porous material aid the capillary transport of water inside the diffusion layer.