Defining precise ecological boundaries and setting clear hydrological benchmarks are critical for achieving sustainable management of groundwater-dependent vegetation (GDV), which plays a vital role in both ecologically significant and highly fragile ecosystems. However, accurately identifying these thresholds remains a complex task. This study applied a space-for-time substitution approach to investigate the eco-hydrological thresholds governing vegetation transitions from GDV to non-GDV states in the hyper-arid Shule River Basin of northwestern China. Extensive vegetation surveys were conducted across approximately 30,000 km2, encompassing diverse environmental gradients within the study region. The survey included 256 systematically sampled plots to ensure robust data representation. Using a combination of diversity indices (species, functional, and phylogenetic), cluster analysis delineated five distinct vegetation communities, with altitude and water table depth (WTD) emerging as the strongest drivers of community composition. Threshold Indicator Taxon Analysis (TITAN) identified twelve plant species-five responding negatively and seven positively to WTD gradients-as effective indicators for distinguishing between GDVs, non-GDVs, and their transitional states along hydrological gradients. The study revealed critical transition zones at WTD ranges of 9.16 to 11.04 m, with a 90% confidence interval extending from 3.79 to 15.41 m. These thresholds are intricately linked with the varying adaptive capabilities of the indicator plant species to WTD gradients, marking the hydrological boundaries between GDVs and non-GDVs. The shallower and deeper zones indicate the niche optima WTD for the GDVs and non-GDVs, respectively. Thus, for practical groundwater regulation, managers should interpret the thresholds by incorporating both the biotic indicators and their associated WTD intervals into adaptive management strategies. This study presents a reproducible TITAN-based methodology for determining dryland vegetation thresholds, with the identified eco-hydrological thresholds offering valuable scientific insights for regime-shift warning systems and conservation planning, and informing sustainable groundwater management strategies in arid regions globally.