The soils in the hyper-arid core of the Atacama Desert (Chile) harbor substantial quantities of soluble salts, including sulfates and nitrates. Gypsum (CaSO₄∙2H₂O) is a prevalent mineral in the Atacama region. It manifests as ∼10-cm-thick surface crusts exhibiting a spatial pattern resembling polygons, in mixtures with other minerals beneath the surface (<3 m deep) or growing in brine ponds of salars. We examine the triple oxygen and hydrogen stable isotopes (δ17O, δ18O and δD) of structurally-bonded gypsum hydration water (GHW) from Atacama gypsum deposits to investigate their formation mechanisms. We observed considerably positive Δ17O anomalies (Δ17O > 1 ‰) in GHW of samples containing substantial amounts of nitrate (generally soil horizons 0.5–2 m deep). This is interpreted as resulting from oxygen isotope exchange between soil nitrate (Δ17O > 15 ‰) and GHW (Δ17O ∼ 0 ‰), either occurring in-situ within the soils due to bacterial activity, or more likely, during cryogenic extraction of GHW at high temperature and low pH in the laboratory. However, when analyzing pedogenic gypsum in soils with negligible amounts of nitrates, the isotopic composition of its parent solution is preserved. These samples showed that gypsum formed from solutions that did not undergo significant evaporation. These waters are isotopically similar to contemporary unevaporated freshwater sources in the region. This indicates that gypsum formation likely occurred through the hydration of anhydrous or hemihydrate calcium sulfate, either in the atmosphere or in the soil. Subsequently, the gypsum was subject to recrystallization in the soil due to occasional rainfall events. This stands in contrast to subaqueous gypsum crystals growing in brine ponds of salars in the Atacama Desert, which reflect the isotopic composition of highly-evaporated parent fluids.