Considering the current development of new nanostructured and complex materials and gels, it is critical to develop a sub-micro-scale sensitivity tool to quantify experimentally new parameters describing sub-microstructured porous systems. Diffusion NMR, based on the measurement of endogenous water’s diffusion displacement, offers unique information on the structural features of materials and tissues. In this paper, we applied anomalous diffusion NMR protocols to quantify the subdiffusion of water and to measure, in an alternative, non-destructive and non-invasive modality, the fractal dimension dw of systems characterized by micro and sub-micro geometrical structures. To this end, three highly heterogeneous porous-polymeric matrices were studied. All the three matrices composed of glycidylmethacrylate-divynilbenzene porous monoliths obtained through the High Internal Phase Emulsion technique were characterized by pores of approximately spherical symmetry, with diameters in the range of 2–10 μm. Pores were interconnected by a plurality of window holes present on pore walls, which were characterized by size coverings in the range of 0.5–2 μm. The walls were characterized by a different degree of surface roughness. Moreover, complementary techniques, namely Field Emission Scanning Electron Microscopy (FE-SEM) and dielectric spectroscopy, were used to corroborate the NMR results. The experimental results showed that the anomalous diffusion α parameter that quantifies subdiffusion and dw = 2/α changed in parallel to the specific surface area S (or the surface roughness) of the porous matrices, showing a submicroscopic sensitivity. The results reported here suggest that the anomalous diffusion NMR method tested may be a valid experimental tool to corroborate theoretical and simulation results developed and performed for describing highly heterogeneous and complex systems. On the other hand, non-invasive and non-destructive anomalous subdiffusion NMR may be a useful tool to study the characteristic features of new highly heterogeneous nanostructured and complex functional materials and gels useful in cultural heritage applications, as well as scaffolds useful in tissue engineering.