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Subterranean or groundwater estuaries occur in porous and cavernous substrates where groundwater abuts the ocean. Like surface estuaries, they are strongly stratified, temporally and hydrochemically heterogeneous environments that support complex hydrogeochemical and biological processes and ecological communities. Here, we contend that groundwater estuaries also occur where groundwater flow approaches salt lakes and provide evidence in the context of groundwater (valley or phreatic) calcretes in palaeovalleys of the arid western plateau of Australia. The calcrete groundwater estuaries display marked and complex physico-chemical gradients along, across and through the groundwater flow path. From the first principles and the density differences between water bodies, we may expect the form and dynamics of the saltwater front to mimic that of marine estuaries but with the dynamic and temporal response to changing hydrology heavily dampened, and driven by the episodic groundwater recharge and lake filling typical of arid regions. The calcrete aquifers support diverse biological communities of obligate groundwater animals, largely endemic to a given calcrete body. These communities comprise both macro and microinvertebrates, predominantly a suite of crustacean higher taxa, and a great diversity of diving beetles (Dytiscidae) isolated in the calcrete aquifers between ca. 5 and 8 million years ago.