Low- or atmospheric pressure RF plasma-enhanced thin film deposition methods are provided for the deposition of hydrophobic fluorinated thin films onto various substrates. The methods include at least two steps. In the first step, RF plasma-mediated deposition is used to deposit a fluorinated film onto a substrate surface. In a second step, plasma-generated active sites on the fluorinated film are quenched by reacting them with stable fluorinated gas-phase molecules in situ, in the absence of plasma, to provide a hydrophobic fluorinated thin film having a very low oxygen content. In some instances the hydrophobic fluorinated thin films have an atomic oxygen concentration of no more than about 3%.