Gas diffusion layers (GDLs) provide pathways for water removal in a polymer electrolyte membrane (PEM) Fuel Cell. Woven GDLs, have shown higher capability to retain water and improve performance under humid conditions compared to non-woven GDLs. In this work, we investigate water transport, distribution and location of breakthrough in woven GDLs using fluorescent microscopy. GDLs with no coating, 30, and 55 wt% fluorinate ethylene propylene (FEP) were investigated. FEP increases hydrophobicity and affects thermal and electrical conductivities. The results show that the FEP-treated GDLs have higher breakthrough pressures and water contact angles than non-treated GDLs. For untreated samples, water breakthrough occurs in non-compressed regions; whereas, for FEP-treated samples emergence occurs in the compressed regions. Furthermore, water was observed to first cover visible pores inside the GDLs prior to breakthrough. Increasing FEP loading promotes the propagation of water inside the GDLs. Thermal conductivity is found to improve with FEP coating and attains a maximum at 30 wt% FEP loading, whereas electrical conductivity decreases with increasing FEP loading. This analysis shows more pores are engaged in water transport with higher FEP loading. Implementation of woven GDLs in fuel cell design requires a balancing of the water and heat transport benefits with the reduced electrical conductivity.