Deserts are distributed in arid areas, and groundwater is the primary source of drinking water and agricultural irrigation for the residents. However, owing to an insufficient understanding of desert groundwater sources, water management policies in arid areas often fail to meet actual water demands. The Badain Jaran Desert is a typical desert with abundant groundwater. However, local economic development has been severely limited due to water resource shortages. To address this challenge, in this study, an integrated approach was utilized to perform a groundwater exploration of the study area. Evidence from δ 2 H and δ 18 O and tracer logging tests in different interdune basins suggests that the desert's groundwater originates from the Qilian Mountains through rapid cross-basin flow and then upwells from hidden volcanic craters in the desert. The deep channels likely comprise contraction joints formed by cooling of the overlying rocks during magmatic diagenesis. Several deserts worldwide receive external recharge from plateaus or mountains rather than from "fossil" water. The initial characteristics of low 87 Sr/ 86 Sr values, which were less than 0.7065, changed with the retention time of groundwater in the aquifer. We conclude that desert groundwater resources have abundant recharge and can meet water demands under a reasonable development approach.