Two oppositely charged water-soluble oligosiloxanes with the same main chain were synthesized and used for the formation of multilayer nanocoatings. In spite of low molecular weight of the components, due to entropic reasons, linearly growing and robust films with a hydrophilic surface were formed for the first time. The multilayer films were found to be resistant to high temperature water treatment undergoing only reversible swelling and no surface recovery was observed after prolonged exposure to air indicating permanent water wettability of these silicone-based coatings. High flexibility of the silicone chains resulted in low glass transition temperature (ca. 27 °C) of both dry polyplexes and films as determined using calorimetry and spectroscopic ellipsometry, respectively. Moreover, the thin coating was applied on plasma-treated poly(dimethylsiloxane) preventing surface reconstruction in air and leading to long-lasting hydrophilization of the surface (water contact angles around 65°). Such water-borne systems may be used in common applications of silicones providing high flexibility and at the same time water wettability of the coatings.