Liquid water transport and oxygen diffusion within the gas diffusion layer (GDL) play key roles in the performance of a polymer electrolyte membrane (PEM) fuel cell. Understanding how liquid water and oxygen are transported through the GDL is crucial for informing future fuel cell material designs. This thesis contains two studies, one numerical and one experimental, that are focused on liquid water and gas transport in GDLs. The first study is an investigation of how liquid and gas transport in the GDL are affected by increasing microporous layer (MPL) intrusion into the carbon fiber substrate. The second study is an examination of the transport mechanisms in the MPL via the fabrication and testing of GDLs that were entirely composed of MPL (called standalone MPLs). Together, these two studies provide a deeper understanding of how novel applications of the MPL can unlock higher performance in PEM fuel cells.