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Recent surveys of groundwater invertebrates (stygofauna) worldwide are yielding rich troves of biodiversity, with significant implications for invertebrate systematists and phylogeneticists as well as ecologists and groundwater managers. What is the ecological significance of this high biodiversity of invertebrates in some aquifers? How might it influence groundwater ecosystem services such as water purification or bioremediation? In terrestrial ecosystems, biodiversity is typically positively correlated with rates of ecosystem functions beneficial to humans (e.g. crop pollination). However, the links between biodiversity, ecosystem function, and ecosystem services in groundwater are unknown. In some aquifers, feeding, movement and excretion by diverse assemblages of stygofauna potentially enhance groundwater ecosystem services such as water purification, bioremediation and water infiltration. Further, as specific taxa apparently play ‘keystone’ roles in facilitating ecosystem services, declines in abundance or even their extinction have serious repercussions. One way to assess the functional significance of biodiversity is to identify ‘ecosystem service providers’, characterise their functional relationships, determine how service provision is affected by community structure and environmental variables, and measure the spatio-temporal scales over which these operate. Examples from Australian and New Zealand alluvial aquifers reveal knowledge gaps in understanding the functional importance of most stygofauna, hampering effective protection of currently undervalued groundwater ecosystem services.