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The investigated Mongolian lakes are marked by a large range of trace element concentrations even in very small geographical areas. This work includes the data on major and trace element concentrations along of a series of samples collected in 2009 and 2012. Three geochemical types of lakes have been distinguished within the study area: (1) alkaline soda lakes, (2) chloride lakes with pH < 9.0 and Na-Cl-dominated composition, and (3) sulfate ones with pH < 8. The soda lakes show high concentrations of As, U, F and relatively low salinity. The chloride lakes have higher salinities and one of them was the most saline of all the lakes (Davsan Nuur). These lakes have higher concentrations of Li (up to 82.1 mg/L), Rb (up to 1350 mg/L), Br and Sr. Sulfate rich lakes are far less common in the area. Characteristic trace elements are Mo, Al and Sr. Thermodynamic modeling at 25°C and 1 bar total pressure was performed with the “HCh” code. We considered mineral and solution equilibria in soda lake waters and calculated the main uranium and arsenic species in solutions and bottom sediments of Shaazgay-Nuur lake to offer a possible way of As removal as an undesirable impurity in commercial products.