The structure and defects of nanodiamonds influence the hydrogen sorption capacity. Positronium can be used as a sensor for detecting places with the most efficient capture of hydrogen atoms. Hydrogenation of carbon materials was performed from gas atmosphere. The concentration of hydrogen absorbed by the sample depends on the temperature and pressure. The concentration 1.2 wt % is achieved at the temperature of 243 K and the pressure of 0.6 MPa. The hydrogen saturation of nanodiamonds changes the positron lifetime. Increase of sorption cycle numbers effects the positron lifetime, as well as the parameters of the Doppler broadening of annihilation line. The electron-positron annihilation being a sensitive method, it allows detecting the electron density fluctuation of the carbon material after hydrogen saturation.