Hydrological niche specialization influences plant survival in hyperarid deserts by allowing species to access different water sources over spatial and temporal gradients. We examined the isotopic hydrological niches of Eriosyce cacti distributed across the arid to hyperarid regions of Atacama Desert. By analyzing stable isotopes (δ²H, δ¹⁸O) in root water, we identified primary water sources and assessed how geographic and morphological factors shape these plants’ strategies to persist under extreme conditions. We characterized the isotopic niche of 323 individuals from 62 populations of 39 Eriosyce species. Our results showed a wide isotopic range. Deuterium excess (D-excess), which indicates evaporation-related enrichment. Species with fibrous roots generally exhibited more negative D-excess, whereas those with tuberous or taproots were associated with more positive values. Coastal and central valley taxa tended showed higher D-excess, reflecting reliance on isotopically enriched fog, while Andean species had more negative values, indicating greater use of rainfall and snow sources. Among the studied taxa, E. aurata var. aurata displayed the broadest isotopic niche, indicating flexibility in exploiting multiple water sources across varying elevations and distances from the coast. In contrast, species such as E. limariensis and E. elquiensis were more narrowly restricted, relying predominantly on a single water source. Bayesian mixing models confirmed that fog dominated as the main water supply for most coastal and central valley species, whereas Andean populations received more substantial contributions from rainfall and snow. Geographic variables—longitude, altitude, and distance from the coast—significantly influenced D-excess, while latitude, aridity index, mean annual precipitation (rainfall), and root dimensions had less impact. These findings demonstrate that Eriosyce cacti employ diverse water-use strategies tailored to local environmental gradients, thereby enabling them to occupy hyperarid desert.