Concern about the effect of rising salinity on freshwater biodiversity has led to studies investigating the salt tolerance of macroinvertebrates and fish, with less attention given to microinvertebrates. We investigated the acute lethal effects of salinity on 12 microinvertebrate species from rivers in the southern Murray–Darling Basin in central Victoria, Australia. For a subset of these species, sub-lethal salinity effects and the effect of water temperature on salinity tolerance were also investigated. The most sensitive microinvertebrates had broadly similar 72-h LC₅₀ values to the most sensitive macroinvertebrates, reported in other studies. However, the most tolerant microinvertebrates tested were much more sensitive than the most tolerant macroinvertebrates and the microinvertebrates studied were more sensitive than most freshwater fish. Temperature affected the acute lethal toxicity of salinity but only to a small degree. In three of four species (the exception being Hydra viridissima), the effects of salinity on growth, development and/or reproduction at concentrations below their 72-h LC₅₀ values were observed. However, different endpoints responded differently to salinity. The demonstrated effect of salinity on microinvertebrates has the potential to indirectly affect fish and salt-tolerant macroinvertebrates via changes to their prey species or ecological functions performed by microinvertebrates.