The analysis of stable isotopes assisted in identifying that groundwater in the Punata alluvial fan is mainly recharged by heavy flash floods, and the recharge from rainfall is of less importance. In addition, the hydrochemical analysis identified the Pucara River as the main source of recharge. Other streams in the north and northwest of the fan do not seem to contribute to the recharge. The hydrochemistry also shows that there is an increase of the Na+ and Cl− concentrations in the middle and distal part of the fan. The salinization of groundwater is most likely a result of the mixing of fresh water with residual saline pore water in the lacustrine deposits and/or ion exchange within these layers. Geophysical surveys assisted in describing the aquifer system layering, and indicated a fine-grained bottom layer where ion exchange might occur. This study demonstrates that the integration of several methods (e.g., hydrochemistry, hydrogeophysics, and stable isotopes) is valuable for clarifying ambiguities during the interpretation process and for characterizing hydrogeological processes in alluvial fans in general.