The role of gas diffusion media with differently structured properties have been examined with emphasis on the liquid water saturation within the cathode of a proton exchange membrane fuel cell (PEMFC). The cathode electrode consists of a gas diffusion layer (GDL), a micro-porous layer and a catalyst layer (CL). The liquid water saturation profiles have been calculated for varying structural and physical properties, i.e., porosity, permeability, thickness and contact angle for each of these layers. It has been observed that each layer has its own role in determining the liquid water saturation within the CL. Among all the layers, the GDL is the most influential layer that governs the transport phenomena within the PEMFC cathode. Besides, the thickness of the CL also affects the liquid water saturation and it should be carefully controlled.