Thin films of fluorocarbon were deposited on polyethersulfone membranes via argon plasma sputtering of a poly(tetrafluoroethylene) (PTFE) target in an RF magnetron plasma reactor. The obtained deposited ultrathin coatings had nanoscale roughnesses and high degrees of fluorination. The intensity of fluorine atom in plasma environment during fluorocarbon deposition was investigated. Depending on the deposition conditions comprising working gas pressure, applied RF power, and distance between the target and the substrate, polymeric films with different chemical compositions and/or morphologies were obtained. The morphologies of the films were analyzed by means of SEM, XPS, and AFM. The results suggested that the sputtered film deposited at a higher pressure and longer target–substrate distance and moderate RF power had a surface composition and chemical structure closer to those of the PTFE film. The treated hydrophobic PES membranes with water contact angles as high as 115° were applied for the first time in an air gap membrane distillation setup for removal of benzene as a volatile organic compound from water. The results showed that the plasma-treated membranes have a comparable or superior performance to that of commercial PTFE used in membrane distillation with similar permeate flux and separation factor after 20 h long term performance.