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Objectives: This study explores whether ancient Atacama Desert populations in northern Chile were exposed to endemic boron contamination. Materials and methods: Using Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS), we studied 144 strands of ancient mummy hair, ranging from 3000 B.C. to 1500 A.D., excavated from the Lluta, Azapa, and Camarones valleys in northern Chile. We tested whether these ancient populations showed signs of significant boron concentration in hair tissue. Results: On average, all individuals from these valleys showed high boron concentrations, ranging from 1.5 to 4 times above the average boron concentration in contemporary hair (baseline <0.85 μg/g). The boron concentration in mummy hair varied according to the main geographic areas mentioned above. Conclusions: The rivers of northern Chile have high geogenic boron concentrations. They contain 38 times above the recommended limit for human consumption. Geogenic boron contamination likely played a role in population morbidity and the types of crops that were cultivated in antiquity. The ancient populations were chronically affected by boron overexposure, suggesting that ancient geogenic water contamination should be considered when discussing the biocultural trajectories of ancient populations.