Abstract: Gonghe basin is located in the soil and water conservation zone of the Yellow river basin ecological reserve. Groundwater is the main water supply source and also the key factor for maintaining the fragile ecosystem in this basin. However, the path of regional groundwater recharge and the mechanism of deep and shallow groundwater interaction are still unclear. Using hydrogen, oxygen and ¹⁴C isotopes, the mechanism of regional groundwater recharge and its indicative effect on ecological environment are discussed in this paper. Results show that lateral infiltration recharge of rivers from Wahong Mountain and Qinghai South Mountain is the main groundwater recharge. The recharge of unconfined groundwater is mainly from infiltration of rainfall after the year 1952 with rapid cyclic alternation and the ¹⁴C age of the confined groundwater is up to 19384.7a.The groundwater characteristics of δ18O, δD and the ¹⁴C age are similar both in the western boundary of the basin and the eastern drainage area, and its recharge source is mainly from ancient water formed during the ice age of 10 000-60 000a ago, which reflecting that there is no obvious hydraulic connection between the Gonghe Basin and the western Chaka Basin. The age of the confined groundwater in the middle of the basin is younger than that in the western boundary and the eastern drainage area. For the middle part of the basin, rainfall and Shazhuyu river infiltration are the main recharge. This study reveals the mutual transformation of recharge-discharge among surface water, unconfined groundwater and confined groundwater in Gonghe basin and is of significance for developing and managing groundwater in this area.