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The investigation of regionally extensive groundwater systems in remote areas is hindered by a shortage of data due to a sparse observation network, which limits our understanding of the hydrogeological processes in arid regions. The study used a multidisciplinary approach to determine hydraulic connectivity between the Great Artesian Basin (GAB) and the underlying Arckaringa Basin in the desert region of Central Australia. In order to manage the impacts of groundwater abstraction from the Arckaringa Basin, it is vital to understand its connectivity with the GAB (upper aquifer), as the latter supports local pastoral stations and groundwater-dependent springs with unique endemic flora and fauna. The study is based on the collation of available geological information, a detailed analysis of hydraulic data, and data on environmental tracers. Enhanced inter-aquifer leakage in the centre of the study area was identified, as well as recharge to the GAB from ephemeral rivers and waterholes. Throughout the rest of the study area, inter-aquifer leakage is likely controlled by diffuse inter-aquifer leakage, but the coarse spatial resolution means that the presence of additional enhanced inter-aquifer leakage sites cannot be excluded. This study makes the case that a multi-tracer approach along with groundwater hydraulics and geology provides a tool-set to investigate enhanced inter-aquifer leakage even in a groundwater basin with a paucity of data. A particular problem encountered in this study was the ambiguous interpretation of different age tracers, which is attributed to diffusive transport across flow paths caused by low recharge rates.