Subaqueous gypsum (CaSO4·2H2O) crystals are relatively common in epithermal systems where sulfide ore deposits are present. The Giant Geode of Pulpí (Almería, SE Spain) hosts some of the largest (up to 2 m in length) subaqueous gypsum crystals discovered to date. Here, we present the first U-series ages of its crystals and reconstruct the oxygen and hydrogen isotopic composition (δ18O and δ2H) of the Pulpí paleo-aquifer from which the crystals formed by using stable isotopes of gypsum hydration water. We successfully dated the onset of gypsum precipitation in the Geode at 164 ± 15 ka. However, the extremely low U concentration (<11 ppb) and relatively high detrital Th content (230Th/232Th < 3.2) hinder accurate dating other gypsum samples. The δ18O and δD values of the paleo-aquifer during the growth of the crystals aligned with the local meteoric water line, suggesting that the sulfate-enriched mother solution consisted of meteoric water that recharged the aquifer during that period. The mean isotopic composition of the Pulpí paleo-aquifer (δ18O = −6.5 ± 0.1‰ and δ2H = −42.3 ± 0.5‰) during the formation of the crystals was similar to the current groundwater in this area (δ18O = −6.1 ± 0.8‰, δ2H = −42 ± 6‰). The isotopic differences observed in samples collected from distinct locations and in individual crystals were probably related to changes in the isotopic composition of the aquifer, as a consequence of varying climate that impacted on the isotopic composition of rainwater during thousands of years in this region. Our results indicated that subaqueous selenite crystals may be useful for paleo-hydrological reconstructions. However, improving the current analytical techniques for dating gypsum with low U concentrations will be essential to obtain accurate and reliable records from Quaternary gypsum cave crystals in the future.