In arid and semi‐arid areas, local precipitation is insufficient to fulfil the water requirements of the fragile local environment; hence, water is obtained from groundwater. The Hulun Lake Basin is located in the Mongolian Plateau, which is home to numerous lakes. In this study, we used remote sensing and isotopic tracing of naturally occurring isotopes (δ18O, δ2H, and 87Sr/86Sr) to identify and quantify the various water inputs into the basin. Based on the lake water balance calculation and precipitation and river inputs, a 5.4 × 108 m3/year groundwater recharge rate was determined. Groundwater and river water with depleted δ18O and δ2H were identified close to the faults near Hulun Lake. The groundwater recharge into Hulun Lake is aided by the faults. The δ18O and δ2H compositions of the groundwater, rivers, and lakes were consistent and more depleted than those of precipitation in the local mountains and plains. Therefore, the rivers and lakes are assumed to be primarily recharged by groundwater. The low strontium isotopes (87Sr/86Sr) in the samples suggest that the water was primarily recharged by basalt groundwater, which was identified under the Cenozoic strata instead of the sandstones, granites, and tuffs, which are the primary rocks in the study area. Moreover, the faults were widely distributed in the study area, allowing for groundwater upwelling from basalts. For the areas with volcanic rocks and faults, particularly in arid and semi‐arid areas, the basalt groundwater recharge through faults is critical for environmental sustainability. This research provides necessary information for future hydro‐ecosystem resource management in arid and semi‐arid areas.