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Saharan paleo-groundwater from the Hasouna area of Libya contains up to 1.8 mM of nitrate, which exceeds the World Health Organization limit for drinking water, but the origin is still disputed. Herein we show that a positive O-17 excess in NO3- (Delta O-17(NO3) = delta O-17(NO3) -0.52 delta O-18(NO3)) is preserved in the paleo-groundwater. The 17O excess provides an excellent tracer of atmospheric NO3-, which is caused by the interaction of ozone with NOx via photochemical reactions, coupled with a non-mass-dependent isotope fractionation. Our Delta(ONO3)-O-17 data from 0.4 to 5.0 parts per thousand (n = 28) indicate that up to 20 mol% of total dissolved NO3- originated from the Earth’s atmosphere (x[NO3-](atm)), where the remaining NO3- refers to microbially induced nitrification in soils. High Delta O-17(NO3) values correspond to soils that are barren in dry periods, while low Delta O-17(NO3) values correspond to more fertile soils. Coupled high Delta O-17(NO3) and high x[NO3-](atm) values are caused by a sudden wash-out of accumulated disposition of atmospheric NO3- on plants, soil surfaces and in vadose zones within humid-wet cycles. The individual isotope and chemical composition of the Hasouna groundwater can be followed by a binary mixing approach using the lowest and highest mineralised groundwater as end members without considering evaporation. Using the delta S-34(SO4) and delta O-18(SO4) isotope signature of dissolved SO42-, no indication is found for a superimposition by denitrification, e. g. involving pyrite minerals within the aquifers. It is suggested that dissolved SO42- originates from the dissolution of CaSO4 minerals during groundwater evolution.