Over the last two decades, Australia has undergone a renaissance in studies of subterranean biology. This paper sets these recent developments into context from the perspective of groundwater fauna. Owing to its obligate subterranean life, typical local endemicity and the geological persistence of subterranean habitats, stygofauna is an excellent subject for biogeographic study. Groundwater containing diverse faunas range from freshwater to marine salinities in both coastal and continental locations. They occur in typical karst, alluvial, and fractured rock aquifers, but also in novel matrices formed during the hydrogeochemical evolution of groundwater (goethite pisolites and groundwater calcretes) in the Tertiary. This range of habitats, water quality and the diverse origins of the fauna (Gondwanan, Pangaean and Tethys) support a phylogenetically highly diverse fauna. Several taxa, notably among the Podocopida, Bathynellacea, Amphipoda, and Dytiscidae show remarkable species diversity. Typically there is fine spatial scale endemicity of species associated with local aquifers, but there are inexplicable regional differences, such as the change of fauna between the Yilgarn and Pilbara, contiguous areas on the long emergent Western Shield. The anchialine taxa representing higher taxa are highly disjunct from their congeners in the North Atlantic. The emerging species richness, the fine scale patchwork of endemicity, and the distinct regional differences, respectively, contribute to a substantial increase in α, β and γ diversity of the aquatic fauna, especially in arid Australia. This diversity is posing challenging issues for proponents and regulators of mineral development because much of this diversity has emerged in the two most mineraliferous provinces of Australia. The scientific capacity to respond is challenged by the sheer scale of the emerging issues.