The flooding, especially in gas diffusion layer (GDL), is one of the critical issues to put PEMFC to practical use. However, the experimental data of the flooding in GDL is so insufficient that the optimization design to solve the flooding problem in GDL has not established until now. In this study we show a method to estimate the water saturation, namely the water droplet occupation for unit volume in GDL. We fabricated a simple interdigitated cell where the supply gas is enforced to flow under rib. This structure made it possible to capture the water droplet in GDL with the measurement of differential pressure through the cell. We operated the cell and measured the differential pressure, and estimated the water saturation with assuming that the flow in GDL is Darcy flow and that the GDL can be treated as sphere packed bed. In addition to deferential pressure measurement, we measured the ionic resistance in polymer electrolyte membrane by AC impedance method. We evaluated the effect of the water saturation on the decrease of cell voltage.