For the last two decades, a rapid eutrophication process impacts Lake Titicaca, the largest tropical freshwater lake in South America and the main highest Great Lake. This is especially notorious in the Bolivian sector of its shallow Lago Menor sub-basin. Lago Menor is deteriorated by the combination of multiple contaminations (domestic, industrial and mining) from untreated wastewater discharged from the urban area of El Alto, indiscriminate overfishing, and climate change. These threats particularly affect the native Andean killifish genus Orestias, the ecology and dynamics of which require in-depth studies with non-invasive techniques.