Central Asia (CA) is susceptible to arid climates and influences from anthropogenic activities. Due to regional differences among plains and mountainous regions in CA, the analysis and comparison of lake pollution levels and responses are essential for attaining a comprehensive understanding of climate change and the timing and intensity of human activities, as well as sustainable development. Here, the elemental geochemistry of sediment cores from three lakes at different elevations during the past 120 years was studied. The results showed that before 1930 AD, the concentrations of potentially toxic elements (PTEs) in the Aral Sea (AS) were comparatively high, and their enrichment factors (EFs) showed moderate to significant enrichment. In contrast, the EFs of PTEs in the two mountain lakes were lower, suggesting zero or minor enrichment driven mainly by natural processes. During the period 1931-2000 AD, the EFs of metals in the AS displayed a decrease followed by an increase, and they were dominantly controlled by agricultural activities. The EFs and fluxes of metals began to rise in Lake Issyk-Kul (LIK), whereas their values in Lake Son-Kul (LSK) remained relatively stable. After 2000 AD, the PTE concentrations further decreased in the AS, but the concentrations of Na, Sr, and Ca increased due to natural evaporation. However, in the mountain lakes, the increases in As, P, and total organic carbon contents in LIK were influenced by agriculture activities, and the EFs and fluxes of Cd and Pb increased in LSK due to atmo-spheric deposition.