Gas diffusion layers (GDLs) are commonly known as one of the critical water management components in polymer electrolyte fuel cells with significant impact on the electrochemical cell performance. Increasing levels of liquid saturation in GDLs, especially during high-current-density operation, limit gas transport from the flow field channels to the catalyst layer surfaces and hence reduce cell performance. To provide GDL material selection and modification guidelines, a thorough understanding of the underlying structural factors of GDL materials and their influence on water management is required. In this work, operando X-ray tomographic microscopy (XTM) was employed to investigate the liquid saturation behavior for three commercial GDL materials during i-E curves and current jump characterization. Liquid volume fractions, saturation profiles and cluster distributions were analyzed to understand observed discrepancies in cell performance. Furthermore, saturation-dependent relative diffusivities were derived via direct numerical simulations, and the impact of GDL substrates on cell performance is thoroughly discussed with respect to structure and thermal properties.