Mongolian saline lakes have been rarely studied. In particular, physicochemical composition of small shallow lakes of the Gobi Desertregion in western Mongolia is simply unknown. Objectives were to characterize chemical composition and describe biogeochemical characteristics of saline lakes in the Gobi Desertregions and steppe mountains, with an emphasis on environmental parameters associated with heavy metal ions. Major physicochemical parameters were determined in 14 lakes (with varying degrees of salinity) located in western Mongolia and associations with geographic variation and distance were determined. Vertical profiles for temperature, specific conductance, and dissolved oxygen were characterized. Salinity and pH were measured with multiparameter submersible profilers. Heavy metal ions (i.e., As, Pb, and Cd) and microelements (i.e., K, Na, Zn, Cu, Ni, Cr, and Co) were analyzed with Inductively Coupled Plasma-Mass Spectrometry. Hydrogen sulfide, ammonia, nitrite, and nitrate were also determined by commercial kits for elemental analysis. Overall, 43 environmental parameters were determined from 31 water samples from various locations, representing distinct geographic features, including Gobi Desert, mountain range and steppe area. Several of these lakes had harmful concentrations of arsenate (< 0.34 mg/L). Heavy metal concentrations were correlated with selected physico-chemical variables of lake salinity and geographic specificity. We inferred that various environmental features, in addition to environmental pollution and mining activity, may be responsible for increased heavy metal concentrations in the Gobi Desert of the western Mongolia. The outcome of this study not only provided insights into lake chemistry, but should also be valuable for water resource management to mitigate potential poisoning and improve public health.