Inka-Coya Lake is located in the Atacama Desert, and this pioneer study characterized the gradient of microbial life along the deep lacustrine sediments that stratified for over 600 years, since the pre-mining period. Our results indicate there are great taxonomic novelty and strong relationships with geochemical composition especially in Cu, Fe, Ni, and V. We propose a clustering of taxa and function in three zones with characteristic taxonomic and functional potential.