Over the past decade, a relatively rich record of neotectonics has been revealed in continental Australia, however very few investigations into the hydrogeological implications have been undertaken. While the most active intra-plate deformation zones are readily identified by seismicity monitoring and satellite and airborne terrain mapping, advances in airborne electromagnetic (AEM) technology and data optimization have made it possible to map numerous, more subtle ‘blind’ intra-plate fault systems concealed in near-surface floodplain landscapes. To date, fault geometries, displacements, and fault zone properties remain ambiguous due to the combination of AEM footprint resolution, the non-uniqueness of the conductivity models and derived hydrostratigraphy and fault geometry solutions produced by AEM equivalent inversion models, and the inherent uncertainty of stitched 1D AEM inversion models. The resultant uncertainty in fault zone characterisation inhibits investigations into the permeability heterogeneity and anisotropy introduced by these faults, making it difficult to resolve the significance of these structures for groundwater processes. In this study, a novel, inter-disciplinary approach has been developed that helps characterise the hydrogeology of one such intra-plate fault zone in unconsolidated, near-surface floodplain sediments. The approach integrates the mapping of tectonic geomorphology, with mapping of sub-surface hydrostratigraphy and ‘blind’ intra-plate fault systems using AEM. Validation of fault zone geometry and displacement at local scales is provided by ground geophysics (e.g. seismic reflection, resistivity and surface nuclear magnetic resonance (SNMR)) and drilling. Fault zone hydrogeology, including permeability variability, has been assessed through the integration of geophysics with hydrochemistry, hydrodynamics, and studies of vegetation response to water availability (using Landsat time-series analysis). A combination of deterministic and stochastic approaches is then used to unravel complex fault zone conduit-barrier system behaviour that determines lateral and vertical groundwater flow, inter-aquifer leakage and recharge. This inter-disciplinary methodology has been used to parameterise numerical groundwater flow models and target potential groundwater resources.