The stable isotope geochemistry of groundwaters from within two intermontane basins of the hyperarid Atacama Desert northern Chile (24º15¢ - 24º45¢S), display distinctly different isotopic compositions related to contrasting morphostructural, geochemical, and hydrodynamic settings. Deep groundwaters from within the northern extent of the Monturaqui Basin (~ 3475 m a.s.l.) are characterised by, high bicarbonate alkalinity (mean of 504 mg/L), low specific conductance (mean=1.91 mS/cm), neutral pH-values, negative redox potentials (mean=-70.0 mV), and mean d³⁴S_CDT and d¹³C_PDB compositions of +3.29 ‰ and –0.84‰ respectively. Groundwaters from the Punta Negra Basin (~ 3200 m) exhibit moderate to low bicarbonate alkalinity (mean of 84.9 mg/L), high specific conductance (mean=12.68 mS/cm), neutral to slightly alkaline pH-values, negative redox potentials (mean=–72.0 mV), and mean d³⁴S_CDT and d¹³C_PDB compositions of +5.8 ‰ and –6.4‰. The combination and range of geochemical parameters measured for Monturaqui Basin are atypical for northern Chile and are thought to be an artefact of localised fumarolic input of volcanic CO₂ and H₂S gases. Punta Negra Basin however, displays isotopic and geochemical data consistent with closed basins throughout the arid Andes.

Values of dD and d¹⁸O for Punta Negra Basin (range of dD_VSMOW=-56.7 to –32.0‰, and d¹⁸O_VSMOW=-6.7 to -2.0‰) waters follow an evaporitic trend typical of closed basin waters in northern Chile and elsewhere. In contrast, dD and d¹⁸O compositions (range of dD_VSMOW=-67.6 to –54.7‰, and d¹⁸O_VSMOW=-8.29 to –7.37‰) of groundwaters from within Monturaqui Basin lie close to the Global Meteoric Water Line (GMWL) and are depleted with respect to dD and d¹⁸O compositions of Punta Negra groundwaters. These isotopic differences are attributed to morphostructural controls on basin hydrodynamics, Punta Negra being a closed basin (internal drainage) and Monturaqui an open basin. Extrapolation from the Punta Negra evaporation line back towards the GMWL gives an intersection at values of d¹⁸O=  -80.3‰ and d¹⁸O_VSMOW=-11.2‰ indicating a recharge source in the high Andes to the east of the basin. Groundwaters from within the Monturaqui Basin are genetically unrelated to groundwaters from within the Punta Negra Basin.