Hydrophobic calcium carbonate (CaCO3) nanoparticles (NPs), modified with dodecanoic acid (DA), are produced and dispersed in solutions of KSE 100, which is a silicic acid ester base product used for the conservation and maintenance of heritage and modern buildings. The dispersions are sprayed on limestone and marble specimens. By adjusting the relative concentrations of DA and NPs, the treated stones obtain superhydrophobic properties. Focusing on limestone it is reported that the treatment has negligible effects on the colour and vapour permeability of the original stone and offers protection against water capillary rise. Several studies are performed to test the durability of the composite (KSE + CaCO3-DA NPs) coating against rain impact, freezing and thawing, salt attack and UV radiation. Moreover, the mechanical, chemical and thermal durability of the coating is studied according to the tape peeling test, contact angles of drops which correspond to a vast range of pH, and heat treatment. The results of the aforementioned tests reveal the very good stability of the composite coating. In sum, it is reported that the wetting properties of the KSE 100 stone strengthener, which is used in building conservation, can be highly improved by adding a small amount of modified CaCO3 NPs. The latter are chemically compatible with calcareous stones.