A microporous layer (MPL) is typically added to gas diffusion layers in polymer electrolyte fuel cells (PEFC) to enhance fuel cell performance and water management. The related transport mechanisms are not completely understood and therefore characterization is required. However accurate determination of MPL liquid water saturation has not yet been broadly addressed, except for preliminary work.We demonstrate that X-ray computed tomography (XCT) is suitable and efficient in characterizing MPL’s local liquid water saturation in an ex situ model experiment setup. Our image evaluation pipeline was first developed on porous polymeric membrane materials, validated by independent gravimetric measurements. Mercury intrusion porosimetry (MIP) on MPL further justifies the efficacy of the method. The pipeline has indicated an accuracy of ca. ±7% and a field of view of 6 mm, which suits differential cell investigations. The linear relationship of greyscale value (GSV) and linear attenuation coefficients is shown to hold even for a polychromatic radiation source. This methodology has the potential to accurately characterize the water saturation in MPLs under operando PEFC conditions.