This study was designed to determine if surface modification via photo-initiated chemical vapor deposition (PICVD) affects the physicochemical properties of polyethylene glycol (PEG) and poly(vinyl alcohol) (PVA) differently, given their different chemical structures and properties. Contact angle measurements showed that both polymers increase in surface hydrophobicity after PICVD treatment. Further, the improved hydrophobicity facilitated dispersion into nonpolar solvents. Chemical changes were concentrated near the surface, evidenced by Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS) measurements, indicating namely that partial oxidation occurs during treatment. These findings were discussed in the context of the difference of the molecular structures of PEG and PVA, which, in turn, control their surface functionalization and hydrophobicity.