A key performance limitation in the polymer electrolyte fuel cell (PEFC), manifested in terms of mass transport loss, originates from liquid water transport and resulting flooding phenomena in the constituent components. A key contributor to the mass transport loss is the cathode gas diffusion layer (GDL) due to the blockage of available pore space by liquid water thus rendering hindered oxygen transport to the active reaction sites in the electrode. The GDL, therefore, plays an important role in the overall water management in the PEFC. The underlying poremorphology and the wetting characteristics have significant influence on the flooding dynamics in the GDL. Another important factor is the role of cell compression on the GDL microstructural change and hence the underlying two-phase behavior. In this article, we present the development of a pore-scale modeling formalism coupled with realistic microstructural delineation and reduced order compression model to study the structure-wettability influence and the effect of compression on two-phase behavior in the PEFC GDL.