Natural stone has been used worldwide in the construction of archaeological and historical heritage. However, its preservation continues to be threatened by weathering and degradation phenomena. Water is widely recognized as the most threatening external component that contributes to stone deterioration, increasing the need for the development of protective hydrophobic coatings to eliminate water penetration. This study intends to contribute to the better understanding of natural stone treatment strategies to prevent water penetration and subsequent stone alteration by studying the effect of coating and stone substrate temperatures, and the number of coating applications, on the effectiveness, compatibility, and durability of commercial hydrophobic coatings. The results obtained revealed that while more than one application increases coating hydrophobic effectiveness, it frequently leads to changes in the aesthetic appearance of natural stone, including whitening and darkening of the substrate’s original hues. Improved hydrophobic effectiveness (maximum gain of ≈ 9%) is also achieved when applying the commercial coatings at 4 °C to natural stone substrates maintained at room temperature, conditions that are feasible to be used in real life. Additionally, the commercial coating composed of silane/siloxane with modified fluorinated additives was found to be the most effective and durable hydrophobic solution.