This study assesses potential geological connections between the unconventional petroleum plays in the Beetaloo Sub-basin, regional aquifers in overlying basins, and the near surface water assets in the Beetaloo Sub-basin Northern Territory, Australia. To do so, we built an innovative multi-disciplinary toolbox including multi-physics and multi-depth imaging of the geological formations, as well as the study of potentially active tectonic surface features, which we combined with measurement of the helium content in water sampled in the aquifer systems and a comparative analysis of the surface drainage network and fault lineaments orientation. Structures, as well as potential natural active and paleo-fluid or gas leakage pathways, were imaged with a reprocessing and interpretation of existing and newly acquired Beetaloo seismic reflection 2D profiles and magnetic datasets to determine potential connections and paleo-leakages. North to north-northwest trending strike slip faults, which have been reactivated in recent geological history, are controlling the deposition at the edges of the Beetaloo Sub-basin. There are two spring complexes associated with this system, the Hot Spring Valley at the northern edge of the eastern Beetaloo Sub-basin and the Mataranka Springs 10 km north of the western sub-basin. Significant rectangular stream diversions in the Hot Spring Valley also indicates current or recently active tectonics. This suggests that those deep-rooted fault systems are likely to locally connect the shallow unconfined aquifer with a deeper gas or fluid source component, possibly without connection with the Beetaloo unconventional prospective plays. However, the origin and flux of this deeper source is unknown and needs to be further investigated to assess if deep circulation is happening through the identified stratigraphic connections. Few north-west trending post-Cambrian fault segments have been interpreted in prospective zones for dry gas plays of the Velkerri Formation. The segments located in the northern part of the eastern Beetaloo Sub-basin do not show any evidence of modern leakages. The segments located around Elliot, in the south of the eastern Beetaloo Sub-basin, as well as low-quality seismic imaging of potential faults in the central part of the western sub-basin, could have been recently reactivated. They could act as open pathways of fluid and gas leakage, sourced from the unconventional plays, deeper formations of the Beetaloo Sub-basin or even much deeper origin, excluding the mantle on the basis of low 3He/4He ratios. In those areas, the data are sparse and of poor quality; further field work is necessary to assess whether such pathways are currently active.