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The physio-chemical and chemical features of water in natural conditions are controlled by the weathering of bedrocks, local climate, landforms and other geo-environmental parameters. In order to understand the characteristics of water and the origins of the dissolved loads in the rivers and in the ground waters of the Taklimakan Desert, western China, we studied the ions in the water samples collected from rivers and wells. We collected water samples from four rivers (Keriya River, Cele River, Tumiya River and Yulongkashi River) in the southern desert and ground water samples from many parts of the desert. Major cations and anions were measured using ion-chromatograph and titration with HCl. The total dissolved solids (TDS), pH and conductivity were examined on site by a portable multi-parameter analyzer. The data show that the water in the rivers of southern Taklimakan is still of fresh water quality and slight alkalinity, although the TDS is comparatively higher than that of many other rivers of the world. The ground water is fresh to slightly saline, with TDS a little higher than that of river water in the study area. The concentration of ions is slightly different between the four rivers in the southern Taklimakan. However, the chemistries of ground water in all samples are to a large degree controlled by sodium and chloride. The ions in the ground water are concluded to be mainly from dissolving of evaporites, consistent with the dry climate in the region, whereas the ions in the rivers are mainly from rock weathering. Low-level human imprints are recognized in the ground water samples also.