The decay diagnosis and conservation of stone-built heritage is becoming a worldwide concern, especially when stone decay causes chromatic changes in the original stone aesthetics, which directly impacts its sociocultural value. Among all the causes of stone decay, water action is identified as the major cause of stone decay and chromatic changes in stone building materials; hence, protective eco-friendly hydrophobic coatings are the efficient and fundamental options to prevent penetrating water into the stone. This paper aims to contribute to tackling water action on natural building stones by studying three different commercial hydrophobic coatings and finding out the correlation between the effectivity, compatibility, and durability of these coatings and the physical, chemical, and mineralogical features of four distinct types of limestone, one calcitic dolomite, four kinds of marble, and one granitoid. Nine different natural stones have been chosen due to their variations in physical, chemical, and mineralogical natures. A multi-analytical approach was adopted through digital microscopy and colourimetry assays to assess the compatibility of the hydrophobic coatings, accelerating ageing in climatic chambers to assess their durability, optical tensiometer analyses to evaluate the hydrophobic effectiveness, and h-XRF and XRPD for determining the chemical and mineralogical composition of stone samples. The results obtained demonstrate that the coating composed of silane/siloxane with modified fluorinated additives (FAKOLITH FK-3 Plus Nano) is the most effective, compatible, and durable coating among the selected hydrophobic coatings. These results can be considered the pioneering steps for developing eco-friendly and cost-effective coatings.