Hydrogen gas (H2) is known for its capability to alleviate detrimental effects of salinity in plants. However, the underlying physiological and molecular mechanisms behind this phenomenon remain poorly understood. In this study, we investigated the mechanistic basis of H2 amelioration of the salt stress in barley (Hordeum vulgare). NaCl addition induced significant inhibition of the root elongation and resulted in a loss of the cell viability; these detrimental effects were substantially reversed by treatment with hydrogen reach water (HRW). Electrophysiological experiments using non-invasive ion flux measuring MIFE technique revealed that the beneficial effects of HRW on salinity tolerance could be explained by (1) higher rate of Na+ extrusion from roots mediated by SOS1-like Na+/H+ exchanger in the root epidermis, and (2) better root K+ retention resulting from ability of HRW-treated plants to prevent NaCl-induced membrane depolarization and reduced sensitivity of K+ efflux channels to ROS. Taken together, these two factors resulted in more favorable Na/K ratio and explained beneficial effects of HRW on salinity tolerance in barley.