The plasma polymerization of hexamethyldisiloxane (HMDSO) leads to the environmentally friendly fabrication of water-repellent coatings through a vapor-phase surface functionalization process using alternatives to the controversial perfluoroacrylate precursors. However, the durability of these coatings is their Achilles’ heel, which requires an in-depth study of the relationship between the structure and properties of these thin films in order to propose concrete solutions for the fabrication of fluorine-free water-repellent textiles. In this context, HMDSO plasma polymers have been deposited on cotton fabrics in an original reactor that allows easy tuning of temporal and spatial parameters of the glow discharge. The functionalized fabrics were characterized to gain insights into the chemical composition of the coatings, their morphology and, above all, their adhesion properties. Interestingly, the results after washing tests revealed a significant dependence of the durability of the superhydrophobic property on the elastic modulus of the deposited polymer. The formation of some radicals at the substrate–thin film interface in the early stages of deposition also correlates with some results. These relationships between the operating conditions of the plasma polymerization, the interfacial properties and the performances of the functionalized fabrics, but also the characterization methodology developed in this work, can undoubtedly serve the engineering of water-repellent fluorine-free coatings on fabrics with optimal durability.