The high-Andean mountain of northern Chile host numerous water systems that is in risk due to increased mining activities. Total and dissolved Cd, Cr, Cu, Hg, Ni, Pb, Se, and Zn in water, and Cd, Cu, Fe, Ni, Pb, Zn, As, Mo, Al, and V in sediments of 21 aquatic systems (rivers, saline lakes, salt flats), were studied. The presence of Pb, Cd, and As in waters and sediments could be explained, in part, by mining activities. Waters are not suitable for human consumption or irrigation due to high content of Cu and As and high pH that exceed Chilean water quality guideline values. The use of different background reference values influences noticeably the conclusion related to environmental quality of sediments, measured with different environmental indexes. The local geological background suggest that Cd, Mo, Pb, and As generate some degree of contamination, while the use of unpolluted systems as background suggest that all metals measured in sediments represent a low contamination risk. The use of background values of local unpolluted systems seems to be more realistic than geological formation or Upper Continental Crust reference values to assess the environmental condition. The ecological risk assessment suggests that Cd and As are threat for communities living in these aquatic environments. However, these systems support abundant wildlife, developing unique extreme ecosystems with great potential for non-consumptive use such as special interest tourism and conservation.