In this paper the a-C:H:SiOx films were synthesized on silicon (100) and glass substrates by plasma-assisted chemical vapor deposition combined with pulsed bipolar substrate bias from mixtures of argon and polyphenylmethylsiloxane vapor. The process of a-C:H:SiOx films formation was investigated by controlling processing conditions such as amplitude of negative pulse of substrate bias and the distance between the substrate and plasma generator. Physico-mechanical characteristics of a-C:H:SiOx films were studied by the nanoindentation technique, atomic force microscopy, Fourier transform infrared and Raman spectroscopy. The contact angle and surface free energy were determined by the sessile drop method using couple liquids (water and glycerin). It was found that the films' properties are interrelated with the density of the ion current on the substrate, which was measured using a guarded planar probe. The obtained results show that film prepared at the smaller substrate/plasma generator distance and optimal substrate biasing has a higher content of sp(3) bonded carbon and, accordingly, has higher hardness, Young's modulus and resistance to plastic deformation. At the same time the a-C:H:SiOx films show large hydrophobicity with a contact angle for water of about 91 degrees and small total surface free energy of about 17.9 mN/m.