A decrease in flow from the iconic travertine mound springs of the Great Artesian Basin in South Australia has led to the oxidation of hypersulfidic soils and extreme soil acidification, impacting their unique groundwater dependent ecosystems. The build-up of pyrite in these systems occurred over millennia by the discharge of deep artesian sulfate-containing groundwaters through organic-rich subaqueous soils. Rare iron and aluminium hydroxysulfate minerals form thick efflorescences due to high evaporation rates in this arid zone environment, and the oxidised soils pose a significant risk to local aquatic and terrestrial ecosystems. The distribution of extreme acidification hazard is controlled by regional variations in the hydrochemistry of groundwater. Geochemical processes fractionate acidity and alkalinity into separate parts of the discharge zone allowing potentially extreme environments to form locally. Differences in groundwater chemistry in the aquifer along flow pathways towards the spring discharge zone are related to a range of processes including mineral dissolution and redox reactions, which in turn are strongly influenced by degassing of the mantle along deep crustal fractures. There is thus a connection between shallow critical zone ecosystems and deep crustal/mantle processes which ultimately control the formation of hypersulfidic soils and the potential for extreme geochemical environments.