Hydrophobic materials are among the most commonly used coatings for building exterior cladding. In fact, these products are easily applied to an existing surface, significantly reduce water absorption and have a minimal impact on the aesthetic properties. On the other hand, although these products have a proven effectiveness, their long-term durability to weathering has not yet been systematically studied and completely understood. For these reasons, this study aims to correlate the effect of artificial aging on the moisture transport properties of hydrophobic treatments when applied on building exterior claddings. Three hydrophobic products (an SiO2-TiO2 nanostructured dispersion; a silane/oligomeric siloxane; and a siloxane) were applied on samples of limestone and of a cement-based mortar. The moisture transport properties (water absorption, drying, water vapor permeability) of untreated and treated specimens were characterized. Furthermore, the long-term durability of the specimens was evaluated by artificial aging, that is, hygrothermal cycles (freeze–thaw and hot–cold). All treatments have significant hydrophobic effectiveness and improve the long term-durability of the treated specimens. However, the results showed that the three hydrophobic products have different effectiveness and durability, with the SiO2-TiO2 nanostructured dispersion being the most durable treatment on limestone, and the siloxane the most suitable for cementitious mortar.