Does the hybridization of the surface of carbon nanoparticles (CNPs) affect the properties of the surface carboxyl and hydroxyl groups and the features of their deprotonation in water? To answer these questions in this work the structures of graphite-and diamond-like carbon cells with OH and COOH groups optimized by the DFT method were studied. It was found that in the same suspensions the OH and COOH groups deprotonate easier being on carbon with sp2 hybridization rather than sp3. Theoretical estimates have shown that in aqueous suspensions of CNPs, “isolated” carboxyl COOH groups on sp2/sp3 hybridized carbon sites have pKa in the ranges of 3.5–4.5/4.5–5, and the hydroxyl OH groups – in the ranges of 8.5–10/15–18, respectively. The conclusions made on the basis of theoretical calculations about the features of deprotonation of surface groups of CNPs are experimentally confirmed by the changes of the zeta-potentials of oxidized detonation nanodiamonds with the change of the pH of the environment.