In the present work, we systematically study the effect of radio frequency induced negative substrate bias voltage, Ub, on the characteristics of CNx films fabricated by direct current (dc) magnetron sputtering of a graphite target in a nitrogen plasma. CNx films, typically 1–2 μm thick, were deposited onto Si(100) substrates at a temperature of 600 °C and at a pressure of 0.5 or 5 Pa. The films’ microstructure and composition were evaluated using elastic recoil detection analysis, Fourier transform infrared spectroscopy, Raman scattering, x-ray diffraction, and atomic force microscopy. The films were found to be amorphous and partially conductive. The nitrogen concentration in the films varied between 12 and 24 at. %. Increasing the |Ub| values from 300 to 700 V resulted in increasing the N/C ratio, while the hydrogen content in the bulk decreased from 5 to 1 at. %. The latter effect clearly demonstrates the sputter-cleaning process during the ion-assisted deposition. Increasing the |Ub| values also resulted in an increase in film density from 1.5 to 2.7 g/cm3, and in a decrease in surface roughness from 13 to 2 nm. This densification was accompanied by an increased hardness (from 2 to 23 GPa), and elastic recovery (from 35% to 74%), and by higher adhesion to the silicon substrate. |Ub| values higher than 700 V lead to the degradation of the films mechanical properties. Even at its low concentration, hydrogen was found to be directly related to the film quality. We suggest that the presence of hydrogen inhibits interconnection of graphite-like planes containing carbon and nitrogen, which may hamper formation of possible fulerene-like microstructure described in recent literature.