Summary Inorganic solute ion concentrations and stable isotopes of oxygen and hydrogen in groundwater, river water and precipitation were investigated to gain insight into the groundwater recharge process in the Kherlen River basin, a semi-arid region in eastern Mongolia. The solute constituents in the river water (main stream) were of Ca–HCO3 type, spatially invariant and low in concentration. Groundwater in the upstream region was also characterized by a Ca–HCO3 type, though all ion concentrations were higher than in the river water. On the other hand, the chemical composition of the groundwater in the midstream region (southern and eastern) was spatially variable and the Na+, Mg2+, Cl− and HCO 3 - concentrations were considerably higher than in the river water and upstream groundwater. The stable isotopic compositions showed an evaporation effect on the groundwater and river water, as well as an altitude effect in the precipitation and river water. Preferential recharge by relatively large rainfall events is thought to have caused the depleted isotopic ratio in the groundwater in the dry regions. The stable isotope, chemical and hydrological data suggest that the main stream water of the Kherlen River is recharged by precipitation that falls in a headwater region at an altitude of more than 1650 m, and that the interaction between the groundwater and river water is not dominant in the midstream and downstream regions of the river basin.