Permeability is one of the fundamental properties of concrete structures as it is strictly related to durability. Mitigation of the degradation processes induced by aggressive solutions can be achieved by controlling water penetration through the pore network. In this study, we test the potential use of nanocomposites as waterproofing agents in concrete. Macroscopic measurements show that the addition of a small amount of nanoparticles effectively reduces the extent of the water permeation front. A combination of experiments, based on X-ray tomography, mercury intrusion porosimetry, and BET nitrogen adsorption, and of numerical simulations, are used to interpret the macroscopic observations. These investigations show that C-S-H precipitation away from cement surfaces, induced by the presence of nanoparticles, leads to a refinement of the pore network. Such a microstructural change in the cement matrix results in a net reduction in the overall concrete permeability.