The concentrations of major ions in the surface water and the groundwater of the Bosten Lake catchment before and during rainy seasons were analyzed to determine the major ion chemistry, geochemical process and to assess the water quality for drinking and irrigation purposes. Natural waters were hard-fresh water with an alkaline nature and a Ca2+-HCO3 (-) water type. Although much of physicochemical parameters were under the highest desirable limits set by the Chinese Government for drinking purpose, some samples were not suitable for drinking with reference to the concentrations of NO3 (-) and SO4 (2-). The sodium adsorption ratio and sodium percentage (%Na) values indicated that most waters were suitable for irrigation. Seasonal variations of ion concentrations and water quality were minor. Saturation index in waters showed that most of the waters were oversaturated with respect to aragonite, calcite, dolomite and magnesite, whereas under-saturated to gypsum and halite. Carbonate weathering and evaporite dissolution were the primary and secondary sources of the dissolved ions, whereas anthropogenic input played a minor role. For the sustainable development of Bosten Lake, a reduction of discharge water from salt washing and an increase in the fresh water inflow to the lake are needed.