Discrete phreatophytic vegetation associated with organic mound springs is present in several places in the semi-arid Walyarta Conservation Park (Park) in northern Western Australia. The mound springs are heritage listed, having significant cultural and environmental significance. Increased industrial (mining and agriculture) development in the region, coupled with a growing demand for groundwater to support these developments, requires an enhanced understanding of how the springs operate and the source of water that sustains their presence. The springs are broadly believed to be situated on geological faults and receive groundwater from artesian sources. However, their association with deeper geological structures and aquifer systems, the focus of this study, is not well understood. This study employed regional- and finer-scale airborne geophysical data, including electromagnetics (AEM) and magnetics, to constrain the sub-basin-scale hydrogeology of the West Canning Basin in Western Australia and to detail tectonic deformation, sedimentological and hydrological processes. The AEM data were inverted using 1- and 2D methods to better define structural discontinuities in the Park, and the results identified the location of faults and other geological structures that were coincident with spring locations. A complementary analysis of spatiotemporal patterns of green vegetation was undertaken using remote sensing data. A model for the extent of green vegetation (in percent), calculated using a constrained linear spectral unmixing algorithm and applied to a select Landsat Thematic Mapper ™ image archive, showed the persistence of green vegetation aligned with interpreted fault systems through extended dry periods. These geophysical and remotely sensed datasets demonstrate that in the Park, the sedimentary aquifers and landscapes are highly compartmentalized and that this constrains aquifer distribution, groundwater quality and the location of wetlands and phreatophytic vegetation. Integrating key information from these datasets allows for the construction of a three-dimensional model that predicts the nature and extent of the critical zone which sustains perennial groundwater discharge within mound springs, drainages and wetlands and provides a framework to assess discharge rates, mixing and, ultimately, sensitivity to changed water availability.