Accelerating demand for energy storage has led to increasing development of brine resources in the “Lithium Triangle”, estimated to hold about 75% of the planet’s Li reserves but persistent and fundamental questions regarding the source and transit time of groundwater have confounded efforts to manage these resources effectively. The basins containing these brines lie within the massive Altiplano-Puna Plateau, home to people whose ancestors have inhabited this land for thousands of years and fragile ecosystems that exist nowhere else on Earth. This region is very dry, bordering Earth’s driest non-polar desert and as such, groundwater is the predominant and, in many areas the only source of water. Fundamental questions about the spatiotemporal dimensions of these groundwater systems have only begun to be addressed. In much of this extreme and remote region, there is a severe lack of quality baseline understanding of the regional hydrological system and connections between surface and groundwater bodies. To address these questions, we utilize an exhaustive set (~2,500 individual analyses) of environmental tracer data (δ18O, δ2H, 3H, 87Sr/86Sr), and dissolved major and minor elements in waters collected from over a dozen field campaigns in the Salar de Atacama and Altiplano of Chile and on the Puna Plateau of Argentina. Our integrated analysis pairs these data with rigorous geochemical modelling and physical hydrological measurements from the field and remote sensing products. 3H data show much of the groundwater currently discharging into these basins is non-modern (>60 yrs. old), stable isotope and geochemical data show strong connectivity but also a marked disconnect between some recharge and discharge areas. We show that “fossil” groundwater, 100-10,000 yrs. or older is widespread and fundamental to the system, sharp disconnects exist between the modern hydrological system, the water bodies it sustains, and those sustained by paleo-recharge water. By defining these connections in spatial detail and within a regional integrated framework, we greatly improve the fundamental mechanistic understanding of this and other groundwater-sustained systems. This will greatly improve the ability of communities, governments and industry to manage of these water resources in a way that is genuinely sustainable.