The Atacama Desert lakes located at high altitudes with very low anthropogenic impacts preserve great potential to recover regional climate changes and environmental processes at a decadal to centennial time scales. Herein, we present a high-resolution analysis of the stratigraphy and metal composition of Inka Coya Lake sediment core, in order to clarify the main forcings acting on sedimentation rates and both eolian and precipitation patterns at Atacama Desert environment. The results suggest that terrigenous inputs can be mainly related to the PDO (Pacific Decadal Oscillation), while laminations preserve a direct association with El Nino-Southern Oscillation – ENSO (4.2–5.3 yr cyclicity). Additionally, the Cu mining activities in Chile are recorded in the lake. The sedimentation rates and precipitation patterns were associated with ENSO, highlighting the relation between La Niña and wetter periods at Atacama. Finally, high-resolution analyses of the geochemical composition provided additional criteria to identify the erosion processes at the basin, suggesting different sources of sediments, which fluxes into the lake covariated with PDO at a decadal scale, especially during the 20th century.