Operating a proton exchange membrane fuel cell (PEMFC) in a planar, open cathode configuration can enable significant reductions in overall device weight and system complexity compared to a conventional fuel cell stack. This decrease in device weight makes an array of open-cathode, planar fuel cells a compelling candidate power source for unmanned aerial vehicles. The flow of ambient air over vehicle-mounted cells can improve oxygen, waste heat, and water transport between the catalyst layer and bulk air. We previously studied the effect of environmental conditions on cell polarization and found that ambient temperature, relative humidity, altitude and air speed all influence cell temperature, which affects water balance and oxygen transport to the catalyst layer. In this work, we relate gas diffusion media (GDM) properties to cell polarization behavior in a broad range of anticipated flight conditions. We study the effect of gas diffusion layer thickness and porosity on cell polarization and discuss its influence on cell temperature, oxygen transport and water management. Similarly, we investigate the polytetrafluoroethylene (PTFE) content in the GDM and the influence of hydrophobicity on cell water management and performance in a broad range of anticipated flight conditions. We use cyclic voltammetry and AC impedance spectroscopy to characterize performance losses associated with GDM properties to guide GDM selection.