We studied an arid, endorheic basin in the Chilean Altiplano to understand how rainfall and evaporation affect groundwater and water availability. Using a rainfall-runoff model and 40 years of satellite data, we found that much of the water evaporates and less reaches the aquifers than expected. Our results challenge the idea that the basin is fully closed and suggest that current water budget estimates may need revision, an urgent task under a changing climate.