Groundwater is an essential source of water for socio-economical development and ecosystem maintenance in Urumqi River Catchment. Special serious problems, such as decline of water level, decreasing discharge, lower Lake water level, increasing mineralization, reducing lake-size, degenerating grassland of the swamp and so on, in Chaiwopu basin due to over abstraction. That resulted in charging of groundwater flow system. Therefore, it is very important for research on the groundwater flow system and its recharge, runoff and discharge for reveal present flow system and reasonable exploitation groundwater resources. This study was based on the background information of geology and hydrogeology, combined with difference of groundwater recharge environment and used hydrochemical and stable isotopes methods to trace the groundwater sources. A comprehensive analysis of NO3--Cl-, HCO3--SiO2 and δD-δ18O of groundwater samples in discharge area was used to identify different groundwater flow system from the different discharge areas including the East Mountain, the South Mountain and the West Mountain recharge areas. Moreover, different water flow systems were subdivided further in the same recharge area.