In this paper, we review the three natural contaminants (arsenic, boron, and lithium) that affected the ancient Andean populations of northern Chile. We debate the natural setting and the toxicity of these elements upon ancient populations exposed and their biocultural significance. This review demonstrates that recent advances in sensitive analytical atomic and mass spectrometry methods have immensely contributed to understanding the extent of exposure to geogenic metal (loid)s by ancient Andeans using well preserved tissues such as hair, bones, and teeth. In addition, the synthesized evidence shows that ancient Atacama Desert populations were significantly affected simultaneously by multiple potentially toxic chronic endemic regional hydro contaminants. Last, we suggest that future archaeometric and archaeological analysis need to consider ancient multicontaminants as an important factor when analyzing diet and health conditions.