The Salar de Atacama is located in the most arid desert in the world. Despite its extreme conditions, it has many ecosystems of high ecological value. The Soncor ecosystem, a sequence of lagoons, is the most important environment of the region as it acts as the centre for the breeding of the Andean Flamingo. This salt flat also contains significant mining deposits and is an important water source for the region. Freshwater and brine-enriched in lithium and potassium-are being pumped from the aquifers near to the Soncor ecosystem, which has so far not been greatly affected by this groundwater extraction. However, there is a potential risk that future anthropogenic effects may disturb this fragile environment. The objective of this study is to determine the origin of the water sources of the Soncor ecosystem so as to adequately manage its water resources. Three hypotheses previously proposed in the technical literature were investigated in order to determine proactive actions to protect this fragile ecosystem. The study utilized classic hydrogeological techniques, such as the construction of stratigraphic profiles, piezometric maps and stream gauging, combined with less-common isotopic techniques, such as the Il existe cependant un risque que cet environnement fragile ne soit affecté par les activités anthropiques futures. La présente étude a pour objectif de déterminer l'origine des eaux de l'écosystème du Soncor afin de gérer convenablement ses ressources en eau. Les recherches ont porté sur trois hypothèses proposées dans la littérature technique, afin de proposer des actions efficaces pour la protection du système. L'étude a mis en oeuvre des méthodes hydrogéologiques classiques comme la construction de profils stratigraphiques, la cartographie de la piézométrie et le jaugeage des cours d'eau, et des techniques isotopiques plus innovantes comme l'étude du rapport 87 Sr/ 86 Sr. Les résultats confirment l'hypothèse selon laquelle l'origine des eaux du Soncor est associée à des apports d'eau souterraine provenant de la partie orientale du salar, dans la zone Nord du bassin.