Arsenic (As) and mercury (Hg) are highly toxic contaminants whereas selenium (Se) is both an essential trace element and potentially harmful at higher concentrations. The hyper-saline lakes of southern Bolivian Altiplano, which are ecological niches for endemic species, are also expected to be enriched in these toxic trace elements. The biogeochemistry of As, Hg, and Se in such high-altitude extreme environments (e.g., high UV radiation and salt content) remains poorly understood. In this study, we investigated the concentrations and chemical forms (speciation) of As, Hg, and Se in sediment, water, and air samples of Lagunas Colorada (LC), Verde (LV), and Blanca (LB) in the South Lipez region (>4200 m a.s.l.). We compared them with the repartition of biodiversity (invertebrates, algae, and bacteria). Extreme As concentrations were found in water (up to 82 mg L -1 ), and the main As species was inorganic As(V), with neither biogenic methylated As nor volatile As forms being detected in water and air, respectively. Se concentrations in water were of 0.1 to 1.4 μg L -1 , and Se existed under different redox states, i.e., Se(IV), Se(VI), and reduced Se (0, -II), including biogenic methylated Se(-II) (trimethyl selenonium). Volatile Se compounds (e.g., dimethyl selenide) were detected in water and air samples. Hg was enriched in the surface water (6 to 30 ng L -1 ) compared to other regional water bodies, and a significant amount of methyl-Hg and gaseous Hg(0) was detected. The drastic disparity between As, Se and Hg concentrations and speciation between lakes has important implications for their cycling in these extreme aquatic systems. While As mostly accumulated in its oxidized and non-volatile form, Hg and Se concentrations can be controlled by significant conversion to reduced and methylated forms, allowing efficient evasion to the atmosphere. Finally, the salinity, including major ions, and high levels of As were among the main drivers of biodiversity repartition between lakes.