Present study examines menisci morphology and percolation behavior of water through the porous fiber matrix of the Gas Diffusion Layer (GDL), and the transport characteristics of droplets according to the energy landscape of the medium. The hydrophobic GDL, which shows promise for improved water management, can be classified as non-wetting (NW), and mixed-non-wetting (MNW, i.e. PTFE coated). The mixed-non-wetting behavior is caused by the hydrophobic coating which allows parts of the meniscus contact line to deform freely in contact with the fibers, while other parts of the meniscus remain pinned due to coating defects. The MNW meniscus is critical to establishing a high breakthrough pressure and a small characteristic droplet volume, setting it apart from both NW and wetting GDL. The main transport mechanism for NW media is by droplet gliding along the fibers, made possible by low adhesion forces. “Clamshell” droplets are energetically favored at high contact angles, optimal design would require small volume droplets yielding low adhesion forces for this morphology. On the other hand, if MNW conditions are present, optimal design should aim for a small droplet volume and high breakthrough pressure as shown in present simulations. The numerical model employed herein captures the meniscus evolution and the corresponding breakthrough pressure for MNW and wetting media, and various degree of pinning. The model predicts up to 50% higher breakthrough pressure when 20% of the meniscus perimeter is pinned, for the MNW medium when compared to the wetting (non-coated) counterpart, results being supported by recent experimental studies.