Fluid flow through the gas diffusion layer (GDL) of fuel cells is numerically studied using a pore network modeling approach. The model is developed based on an experimental visualization technique (fluorescence microscopy). The images obtained from this technique are analyzed to find patterns of flow inside the GDL samples with different hydrophobicity. Three different flow patterns are observed: initial invasion, progression, and pore-filling. The observation shows that liquid water flows into the majority of available pores on the boundary of the untreated GDL and several branches are segregated from the initial pathways. For the treated GDL, however, a handful of boundary pores are invaded and the original pathways extend toward the other side of the medium with minimum branching. The numerical model, developed based on an invasion percolation algorithm, is used to study the effects of GDL hydrophobicity and thickness on the flow configuration and breakthrough time as well as to determine the flow rate and saturation in different GDL samples. During the injection of water into the samples, it is numerically shown that the flow rates are monotonically decreasing for both treated and untreated samples. For the treated sample, however, the injection flow rate is constantly lower than that of the untreated sample, resulting in a lower overall water saturation at breakthrough. The numerical results also suggest that hydrophobic treatment of thick samples has minor effects on water management and overall performance. The developed model can be used to optimize the GDL properties for designing porous medium with effective transport characteristics. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.