Evaporation exerts a dominant influence on groundwater-lake interactions in arid environments, yet its coupling with redox dynamics and trace element mobilization remains poorly understood. Here, we combine stable isotope (delta 2H, delta 18O) and trace element concentration analyses of manganese (Mn), arsenic (As), and barium (Ba) to quantify evaporation intensity and evaluate its geochemical effects in the Badain Jaran Desert, China. These trace elements were selected because they are commonly enriched in arid regions and highly sensitive to both evaporative concentration and redox transformations, posing potential risks to human health. High-resolution sampling along two groundwater transects at South Sumujaran Lake reveals distinct isotopic and geochemical patterns. Deuterium excess (d-excess) and evaporation coefficients jointly indicate that evaporative fractionation is stronger in the oxidation-dominated eastern transect, where evaporation drives Mn and Ba accumulation, whereas in the reduction-dominated western transect, redox-controlled mobilization and desorption lead to As and Ba enrichment. At the regional scale, Bayesian isotope modeling of lakes across the Badain Jaran Desert indicates that pre-evaporation delta 18O decreases and the evaporation coefficient increases from southeast to northwest, reflecting regional gradients in precipitation, continentality, and aridity. The lakes are sustained primarily by local and mountain-block groundwater recharge, with about 91% occurring under reducing conditions that enhance trace element mobility. These findings provide a process-based understanding of how coupled evaporative and redox processes regulate isotopic evolution and solute dynamics in desert aquifers and highlight the growing vulnerability of groundwater quality in arid regions under intensified evaporative stress.