The detachment processes of the hydrogen (H) and deuterium (D) plasmas are comparatively investigated in the linear plasma device NAGDIS-II. The laser Thomson scattering measurements demonstrate that the recombination rate of the H plasma is greater than that of the D plasma as the neutral pressure increases in the molecular activated recombination (MAR) dominant detachment phase. As the recombination process by MAR is strongly dependent on the vibrational and rotationally excited states of the molecule, the rovibrational quantum state populations of the H and D molecules are measured using the Fulcher-α band spectroscopy. The results indicate that the vibrational temperature in the electronic ground state is considerably higher than the rotational temperature during detachment. The reaction rate coefficients for MARs due to charge exchange chains (CX-MAR) and dissociative attachment chains (DA-MAR) are calculated by the collision-radiation model under the measured temperature conditions. It can be observed that the CX-MAR is larger than the DA-MAR for both H and D, and that the CX-MAR of H is larger than the CX-MAR of D at electron temperatures Te above 1 eV. In consideration of the experimentally observed vibrational and rotational excitation temperatures, the reaction rate coefficients of CX-MAR and DA-MAR are increasing in the low Te region. These calculations are in accordance with the experimental results, which indicate that recombination processes due to MAR are more predominant in the H plasma compared to the D plasma. Furthermore, a transition from MAR to electron–ion recombination processes is observed in the D plasma at Te below 0.5 eV.