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In the arid region of northern Xinjiang, one of the least-studied areas in China, three watersheds, namely those of the Yili, Zhungarer and Erlqis, have become the focus of attention due to rapidly increasing human population and water demands. The hydrogeochemistry of natural water from the three watersheds was investigated. The ionic chemistry of natural waters from these watersheds changes considerably on a regional scale. The waters are neutral to alkaline in nature and most of them are soft-fresh waters. The total dissolved solid (TDS) varies over two orders of magnitude with a mean value of 580 mg/L, about 1.2 times and 4.6 times those of the Huanghe (Yellow River) and the world spatial median, respectively, but only 40% and 0.8% of those of the Tarim and the western Alashan watersheds, respectively. Much of the solutes and physicochemical parameters in these waters are under the highest desirable limits of the World Health Organization (WHO) for drinking purpose and a plot of sodium adsorption ratio versus EC shows that most waters are of good water quality for irrigation. Water-rock interaction and saturation index (SI) for selected minerals are evaluated. The SI of these natural waters is out of equilibrium (undersaturated) with respect to major carbonates (calcite and dolomite) and evaporites (gypsum and halite). The high concentrations of alkali earth metals, alkalinity and the high (Ca + Mg)/(Na + K) and Na/Cl ratios indicate that the release of major solutes in these waters is controlled largely by dissolution processes of carbonate and partly by silicate weathering, while, cation exchange reactions, soil-salt leaching and evaporation processes also play an important role. The effects of local pollution are minimal in the montane and piedmont areas of these watersheds but are significant in the oases and central areas of the drainage basins. (C) 2011 Elsevier Ltd. All rights reserved.