Transport of water through the gas diffusion layer (GDL) is explored to simulate the water flow in the cathode of a proton exchange membrane fuel cell (PEMFC). In this study, several commercial GDL media, including carbon paper and carbon cloth with or without a microporous layer (MPL), are employed. Liquid water is injected through the GDL media, and the differential pressure drop is measured to analyze the dynamic features of the water flow through the different structures of the GDL samples. Moreover, by combining the top-view images of the water droplet that emerges out of the GDL with the results of the dynamic measurement of the differential pressure drop, the water saturation inside the GDL after the water breakthrough through the GDL is analyzed. The “self-eruption transport” mechanism, which may control the water contained inside the GDL regardless of the water generation rate, is observed in the GDL whose one side is treated with MPL only. This suggests that a GDL with single-side MPL treatment may help effectively water management.