We examined the variation of stygofauna composition collected in wells, along a gradient in groundwater salinity/conductivity in a coastal aquifer from southern Portugal. The studied coastal aquifer is considered vulnerable to salinization due to seawater intrusion, caused by overexploitation of the aquifer. Knowing the response of the stygofauna species to present levels of groundwater salinity makes it possible to understand and measure the effects of saltwater intrusion on stygofauna, rendering them potential bioindicators of this environmental pressure. Biotic and abiotic sampling was conducted in six shallow wells located in the fresh–saltwater interface of the Arade estuary along the salinity gradient established in the groundwater from the estuary to inland locations (microSiemens/cm). Groundwater salinity was highly correlated with taxa distribution. The stygobites Eucyclops hadjebensis and Acanthocyclops sensitivus, the cosmopolitan Megacyclops viridis and Cypria ophtalmica were particularly associated with low-salinity conditions, whereas Eucyclops graeteri, Megacyclops brachypus and Daphnia pulicaria were related to high-salinity waters. Multivariate analyses indicated that stygofauna assemblages varied significantly with location. We suggest that stygofauna composition and structure can be a useful complementing tool for monitoring seawater intrusion into coastal aquifers, where reduction or deterioration in groundwater resources is predicted.

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