Detailed information on groundwater recharge and flow is vital for the proper management of groundwater resources in the arid area.Natural stable and radiogenic isotopes of water have been widely and extensively used over the last forty years to probe into problems related to the groundwater recharge and flow system.The present study aimed at the integration of a variety of isotopic measurements for analyzing the recharge and flow of the groundwater system in the Jiuquan-Zhangye Basin.The tracer data suggest that the recharge water of the basin is drived from the drainage of mountain rivers. Recharged to the aquifer occurs through the high permeability recharge zone in the piedmount area. Groundwater in the alluvial fan zone seems to be rapidly recharged water from the infiltration of mountain rivers since 1963, whereas some groundwater within the confined aquifers was recharged before 1952. The tracers also indicate that there are two groundwater flow systems, i.e., regional and local flow systems, and there are no significant hydrodynamic contact between the Jiuquan Subbasin, i.e., regional and local flow systems, and there are no significant hydrodynamic contact between the Jiuquan Subbasin and the Zhangye Subasin. The common features establish can not only serve as a case study but also contribute to the groundwater resourse sustainable development in similar inland areas.