[1] Local porosity theory in combination with percolation theory was applied to shale microstructures that were reconstructed on the basis of focused ion beam nanotomography and scanning transmission electron microscopy. This allowed characterizing pore microstructures in Opalinus clay with length scales on the order of tens of microns. In a sample from the sandy facies (with low clay content), the fraction of “larger” pores ϕ(radii~ > 15 nm) = 0.076 is substantially higher than that in the shaley facies (with a higher clay content), where ϕ(radii~ > 15 nm) = 0.015. The resolved porosity possesses a certain degree of homogeneity, and the representative volume element (RVE) of porosity can be determined in terms of a given relative error on porosity. For example, if we accept a relative error of 10%, the RVE is on the scale of a few hundreds of microns. Both pore microstructures from sandy and shaley facies show anisotropic characteristics with respect to connectivity and percolation threshold. Using finite scaling, we found percolation thresholds with critical porosities ϕc,b = 0.04–0.12 parallel to bedding and ϕc,perp = 0.11–0.19 perpendicular to bedding. The resolved porosity of the sandy facies (low clay content) is close to the percolation threshold, whereas the porosity of the shaley facies (high clay content) is below the percolation threshold. The porosity in carbonate layers is around ϕ = 0.027, and the pore size is substantially larger when compared to the pores in the clay matrix. In the analyzed sample, pores in carbonate layers are poorly connected.