Plasma chemical surface modification of nanoparticles in gas-liquid type reactors enables a controllable, specific, low-cost, and environmentally friendly alternative to wet chemistry methods or thermal and dry plasma treatments. Here the atmospheric pressure radio-frequency microplasma jet (µ-APPJ) operating with 0.6% O in He is used to deliver aqueous oxygen radicals (AOR) to the surface of ∼3 nm hydrogenated detonation nanodiamonds (H-DNDs) suspended in water. The AOR-treated H-DND samples are characterized by FTIR and XPS spectroscopies and by AFM and SEM imaging. The main chemical reaction mechanism is identified as the abstraction of surface hydrogen atoms by O or OH radicals and a consequent attachment of the OH group, thereby increasing concentration of alcohols, carboxyls, and aldehydes on the DND's surface. FTIR spectra reveal also a structural re-arrangement of the surface water on the AOR-treated H-DNDs. Yet zeta-potential of AOR-treated H-DNDs still remains positive (decreases from +45 mV to +30 mV). The chemical modification gives rise to formation of nanoscale chain-like aggregates when AOR-treated H-DNDs are deposited on Si substrate.