Water resources are the most critical factors to ecology and society in arid basins, such as Kaidu River basin. Isotope technique was convenient to trace this process and reveal the influence from the environment. In this paper, we try to investigate the temporal and spatial characteristics in stable isotope (18O and 2H) of surface water and groundwater in Kaidu River. Through the water stable isotope composition measurement, spatial and temporal characteristics of deuterium (δ2H) and oxygen 18 (δ18O) were analysed. It is revealed that (1) comparing the stream water line with the groundwater line and local meteorological water line of Urumqi City, it is found that the contribution of precipitation to surface water in stream runoff is the main source, whereas the surface water is the main source of groundwater. Groundwater is mainly drainage of surface runoff in the river; (2) in the main stream of Kaidu River, the spatial variability of river water showed a ‘heavier-lighter-heavier’ change along with the main stream for δ18O, and temporal variability showed higher in summer and lower in winter; (3) the δ18O and δ2H values of groundwater samples ranged from −11.36 to −7.97‰ and −73.45 to −60.05‰, respectively. There is an increasing trend of isotopic values along the groundwater flow path. The seasonal fluctuation of δ18O is not clear in most samples. Copyright © 2012 John Wiley & Sons, Ltd.