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Northern Chile has scarce water resources due to the Atacama Desert. Thus, water obtained from The Andes range has great interest. This study analyzes the effect of different amounts of irrigation water on gas exchange, seed yield, biomass and water use efficiency in two chia (Salvia hispanica L.) phenotypes, white and black. We performed measurements during flowering and at physiological maturity. The experiment was installed in field conditions under three water regimes: 100, 70 and 40% of the evapo-transpiration portemntial (ETo). No significant differences were found in gas exchange parameters among treatments, but there were differences between sampling times, decreasing as a function of senescence. Intrinsic water use efficiency (WUE-intr) was not different between treatments or on the two measuring dates in either phenotype, except for black in the treatment with least water. The water use efficiency in biomass production (WUE-biomass) did not show significant differences between treatments in either phenological stage. Seed yield was not significantly different between treatments in white chia, while in dark chia seed yield increase was directly related to water availability. In both phenotypes, the WUE referring to seed yield (WUE-seed) was significantly greater in plants with less water availability.