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The Middle Awash basin is an arid region in Ethiopia where surface waters are scarce and local communities are dependent on groundwater resources for water supply. The complex hydrogeological system of this basin has been conceptualized. Multivariate statistical analysis of hydrochemical variables and water isotopes were used to study the rock-water interaction, geochemical reaction processes and the hydrological link between aquifers. Groundwaters from aquifers of the high-rainfall plateau bounding the rift are slightly mineralized, as well as depleted in delta O-18 and delta D, and contain H-3 above 0.8 TU. This suggests a low degree of rock-water interaction and that groundwater is under recharge from heavy rain that falls on surrounding highlands. On the other hand, groundwaters from aquifers of the rift floor are highly mineralized and show slight enrichment in delta O-18 and delta D with positive oxygen shift, but contain H-3 below 0.8 TU. The positive oxygen shift in rift floor groundwaters may be caused by the isotopic exchange of oxygen between groundwater and aquifer materials during rock-water interaction, whereas the low H-3 content could be due to the decay of tritium along relatively long flow paths. The approach utilized in this study may be applicable to understanding hydrogeochemical processes in other complex volcanic terrains.