Over the last century, the Atacama Desert has been exploited due to the mineral resources in this environment. These anthropogenic effects have primarily been linked to the development of the mining industry, the impact of which remains uncertain. Here, we use high-resolution geochemical characterization and magnetic properties analysis from the sedimentary core of Inka Coya Lake, located in the Atacama Desert, to assess the anthropogenic impact in this metallogenic region. The geochemistry and magnetic properties changed with core depth. Elements, such as Cu, Ni, and Zn, increased during the lake's most recent period.Additionally, an increase in mass magnetic susceptibility (χ) and a decrease in magnetic susceptibility depending on the frequency (χfd%) may be attributed to fine iron oxide grains originating from industrial and urban sources. Moreover, indices of pollution classified the sediment of Inka Coya Lake as slightly polluted and strongly polluted with Ni, and Cu, respectively. This could reflect a period of pollution caused by the increase in the production of copper sulfide. These results highlight the possible impact of mining activities in the hyper-arid core of the Atacama Desert, which affects surrounding areas through dispersive processes, even reaching high altitudes, and provides a scientific basis for the prevention of environmental pollution from mining and the protection of the sediment and water source in the Atacama Desert.