Estimating groundwater recharge in arid regions with seasonal snow cover, as in the Andean Altiplano of northern Chile, is important for sustainable development policies and the effective management of scarce resources in a high water demanding zone, as fragile ecosystems depends on a stable water contribution. This research aims to evaluate and quantify rainfall and snowfall contribution to aquifer recharge while assessing the factors that control the hydrodynamics in such areas, based in the knowledge of the better documented Tuyajto Lake in the Tuyajto catchment/basin. The modeling framework involves an energy balance of the snow cover, a soil water balance and a groundwater flow and chloride transport model. The basin average annual recharge is about 23% of average precipitation. Snowmelt contribution to recharge is important at altitudes above 4700 m a.s.l. during September, while rainfall is more important in February and March, during short intense precipitation events. The hydraulic conductivity of ignimbrites and other volcanic formations are the most important hydrogeological parameters controlling lake level and spring flow rates, while albedo and snowpack surface roughness length on the energy balance causes the greatest variation of lake level. Evaporation is the process controlling the variability of the lake level, as aquifer contribution remains relatively constant and springs flow variability is not enough to cause the observed variations, except during November. Possible buried salts deposits on the eastern edges of Pampa Colorada and Tuyajto Lake, together with volcanic HCl contribution, justify the high measured groundwater chloride concentrations. A recharge 2-3 higher than the current one is necessary to justify a lake level 40 m above its modern value during the Last Glacial period, giving insight into past hydrological changes in the basin due to climate variability. The knowledge gained can be applied to other high altitude volcanic basins with seasonal snow cover.