Aridity and seasonality of precipitation are characteristics of the highland region in Bolivia. Groundwater becomes an important and safe source of water when surficial bodies are intermittent and affected by natural and anthropogenic contamination. Decades of exploitation of the Challapampa aquifer, combined with lack of information required to understand the groundwater circulation, represent a challenge for reservoir management. This study analyzes isotopic compositions of deuterium and oxygen-18 in different stages in the hydrologic cycle to assess flow patterns in the aquifer, especially in the alluvial fan of River Paria, where records are more extensive in space and time. Interpretations are based on existing and new data. Some implications, such as the age of water, the evaporation effect in groundwater and some thermal intrusions are supported by stable isotopes, tritium, radiocarbon, and electrical conductivity records. New results confirm that modern precipitation over the mountains surrounding the study area is the most important origin of water for shallow aquifers until exploited depths, 100 m below surface. The origin of water in deeper depths, 400 m, seems related to infiltration at higher altitudes and longer residence times.