The effective diffusion properties of a gas diffusion layer (GDL) made of the assembly of a fibrous gas diffusion medium (GDM) and a microporous layer (MPL) are characterized from numerical simulations on reconstructed images obtained from combining micro X-ray computed tomography and focused ion beam-scanning electron microscopy (FIB-SEM). Using a multiscale approach, the MPL effective diffusion tensor is characterized from the FIB-SEM reconstructed 3D images considering Knudsen and Fickian diffusions. The GDM-MPL assembly effective through-plane diffusion coefficient is computed via a mixed approach combing a continuum description for the MPL and the explicit consideration of the MPL cracks and GDM fibers. The impact of cracks in the MPL is thus evaluated. A diffusive resistance model is developed to evaluate the impact of the MPL penetration into the GDM and the impact of the GDM compressibility.