The giant nitrate deposits of the hyperarid Atacama Desert (Chile) are one of the most extraordinary, yet enigmatic, mineral occurrences on Earth. These deposits are complex assemblages of highly soluble nitrates, chlorides, sulfates, perchlorates, iodates, and chromates, and their preservation is the result of prevalent hyperarid climate conditions in the Atacama Desert since the late Miocene, with average rainfall rates of <10 mm/yr in the past ∼3 m.y. Although several hypotheses have been proposed since the mid-1800s, the formation of these extensive deposits still remains highly controversial despite the fact that recent studies have argued toward an atmospheric source for the nitrate, sulfate, and perchlorate components. In this report, we focus on the often overlooked and poorly studied iodine and chromium components of Atacama’s nitrates. We present the first cosmogenic iodine (129I) and stable chromium (δ53/52Cr) isotope data of nitrates showing that groundwater has played an unforeseen role in the formation of these massive deposits. The isotopic signature of I in the nitrates (129I/I ∼150–600 × 10–15) share similarities with deep sedimentary (marine) pore waters and shales, deviating significantly from atmospheric iodine (129I/I ∼1500 × 10–15), while the positive and highly fractionated δ53/52CrSRM979 values (+0.7‰ to +3‰) are indicative of intense Cr redox cycling due to groundwater transport. Our evidence points toward a multi-source genetic model for the Atacama Desert nitrate deposits, where these extensive accumulations were the result of long-lived, near-surface mineral precipitation driven by groundwater (i.e., chromates, iodates) coupled with dry atmospheric deposition (i.e., nitrates, perchlorates) and sea spray inputs (i.e., sulfates, chlorides), triggered by increasing aridity and tectonic uplift.