The geothermal potential of the Sembalun region was assessed by several scholars but none specifically studied the elevation of the recharge area. The concept is important because the sustainability of geothermal system significantly depends on the presence of meteoric water supplies that infiltrate the recharge area. Therefore, this study aims to determine the elevation of the recharge area for the thermal water and the control mechanism of sub-surface water flow at the Sembalun geothermal system. Three units of bulk equipment were placed at three different elevations above sea level and a total of 30 rainwater samples were periodically measured in volume and stable isotope content of 18O and 2H. The isotope analysis of Sebau Hot Spring, Orok Warm Spring, and monthly rainwater samples showed that the elevation of the recharge area for the Sembalun geothermal system ranged from 1360 to 1500 m above sea level (masl) and originated from the hilly regions at the south and southeast of the Sebau geothermal manifestation. Hydrogeologically, the meteoric water infiltrated through the fracture systems in the several lava and pyroclastic rocks formed due to numerous eruption periods.