We report here on a robust and easy-to-implement method for the labelling of detonation nanodiamonds (DND) with hydrogen isotopes (deuterium and tritium), using thermal annealing performed in a closed system. With this method, we have synthesized and fully characterized (FTIR, Raman, DLS, 3H/2H/1H and 13C MAS NMR) deuterium-treated and tritium-treated DND and demonstrated the usefulness of isotope incorporation in investigating the surface chemistry of such nanomaterials. For instance, surface treatment with deuterium coupled to FTIR spectroscopy allowed us to discriminate the origin of C-H terminations at the DND surface after the hydrogenation process. As a complementary, tritium appeared very useful for quantification purposes, while 1,2,3H NMR confirmed the nature of the C-1,2,3H bonds created. This isotopic study provides new insights into the characteristics of hydrogen-treated DND.