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Complementary analysis of satellite mission data (altimetry, Moderate Resolution Imaging Spectroradiometers (MODIS)) and climate fields over 2000–2009 was conducted to investigate the variability of the water cover surfaces and the geographical source of water inflowing into the Lake Poopó system. The results suggest that over the time span of 2000–2009 a great part of the variability of the Poopó system originates from geographic sources other than Lake Titicaca. Possible alternative causes include climate change inducing increased temperatures and greater evaporation rates along the Altiplano; increased glacier and snow melting over the Andes Cordillera; and a potential increased anthropogenic water use (such as irrigation, minery, etc.) throughout the path of the Desaguadero River (which connects lakes Titicaca and Poopó). This change in the hydrology of this region could lead to a collapse of water supplies and endanger the already fragile Poopó system as well as the regional socioeconomic system, which closely depends upon it.