Poly(ethylene-co-vinyl alcohol) (EVOH) films with two different ethylene contents (29 and 44 mol %) have been treated by hydrophobic plasma (CF4, tetramethylsilane (TMS), CF4/H2, and CF4/C2H2). Conditions of the cold plasma treatment were optimized by the water contact angle measurements as a function of the different plasma parameters (plasma power, gas flow, and treatment time). Chemical changes of the film surface were characterized by X-ray photoelectron spectroscopy. The obtained results revealed the presence of fluorine containing functional groups such as CF, CF2, and CF3 in the case of CF4, CF4/H2, and CF4/C2H2 plasma treatment and the presence of SiOxCy compounds after TMS treatment. The morphology of the plasma treated EVOH films was examined by atomic force microscopy, which indicated an increase of the film roughness after treatment. Negligible changes of thermal properties of the modified EVOH films were observed by means of the temperature modulated differential scanning calorimetry. The barrier properties of films were characterized by water permeability measurements. It was found that the hydrophobicity was significantly improved after plasma treatment and for some treated films the water permeability was decreased up to 28%.