Anthropogenic impacts in groundwater ecosystems remain poorly known. Climate change is omnipresent, while groundwater salinization poses serious long-term environmental problems in arid and semi-arid regions, and is exacerbated by global warming. Both are present threats to the conservation of groundwater ecosystems, which harbour highly specialized species, with peculiar traits and limited geographic distributions. We tested the temperature and salinity tolerance of groundwater-adapted invertebrates to understand the effect of global warming and salinization in groundwater ecosystems. We used species representative of groundwater-adapted crustaceans: two copepods (harpacticoid and cyclopoid) and one syncarid, endemic to Australia. Our results show that 50% of the populations died at salt concentrations between 2.84 to 7.35 g NaCl/L after 96 h, and at 6.9 °C above the ambient aquifer temperature for copepods and more than 10 °C for syncarids. Both copepods were more sensitive to temperature and NaCl than the syncarid. We calculated a salinity risk quotient of 9.7 and predicted the risk of loss of 10% of syncarid and 20% of copepod population abundances under a worst-case scenario of global warming predictions for 2070. These results highlight that both salinity and temperature increases pose a risk to the ecological integrity of groundwater ecosystems.