The White Paper on Developing Northern Australia, released by the Australian Government in 2015, provides a long-term vision for sustainable economic development in the north. This vision recognises the importance of water availability for key industries, including agriculture, aquaculture, mining, energy and tourism. However, it also notes that there are substantial knowledge gaps around northern surface water and groundwater systems. The 2018 report of the Pepper inquiry into hydraulic fracturing activities in the petroleum industry in the NT highlights the lack of knowledge of the aquatic ecology and biodiversity of surface and groundwater systems, particularly in the semi-arid and arid regions of the NT. To address these critical knowledge gaps, aquatic surveys have been undertaken within the Beetaloo Sub-basin, and nearby areas, where environmental and hydrological impacts associated with the emerging shale gas industry may occur. What has been found find so far? A study of groundwater wells (bores) undertaken in 2019 revealed previously unknown stygofaunal and microbial communities in the karstic habitats of the Tindall limestone aquifer that lies beneath the Beetaloo region. The stygofauna, dominated by Crustacea, contains at least 11 new species, and possibly more. A survey of surface waterbodies (rivers and wetlands), across four catchments (the Daly, Roper, Limmen Bight and Victoria River-Wiso) in 2020 and 2021, detected five species of freshwater turtles, 30 species of fish and 195 species of aquatic invertebrates. More than 20% of the latter appear to be new to science and 40% are new records for the region. Are these freshwater survey results sufficient to redress the knowledge gap and inform environmental management and policy? Possibly, if the new species are described. Additionally, more targetted studies are needed to ensure that the spatial and temporal variability of these systems, and the biota they support, is better understood.