Proton Exchange Membrane Fuel Cell (PEMFC) technology has been receiving more attention recently and can play a more expanded role in space missions with low gravity or microgravity. The liquid water generation in the Gas Diffusion Layer (GDL) of a Proton Exchange Membrane Fuel Cell (PEMFC) increases the resistance to oxygen flow toward the catalyst layer. Water flooding inside the GDL can affect the PEMFC performance especially at higher current densities. Therefore, a good understanding of the effect of liquid water amount in the GDL is crucial to water management and, subsequently, to the performance of the fuel cell. The purpose of the present study is to investigate the effect of the microstructure characteristics of the GDL on the water flooding and liquid water distribution inside the GDL. A one-dimensional theoretical model has been developed. Results indicate that the porosity gradient has a significant effect on the liquid water saturation and the performance of the PEM fuel cell.