1. Glacial relict mysid and amphipod crustaceans are characterised by their affinity for cold and well-oxygenated waters and inability to disperse upstream or by external agents. These crustaceans occur in large and deep lakes of Northern and Central Europe and North America, their distributions shaped by glaciation events. In Europe, along the southern edge of their distribution (Germany, Poland, Lithuania, Belarus), glacial relict crustaceans are threatened by eutrophication and global warming. 2. This study assesses the status of three glacial relict malacostracan species in Lithuania; the amphipods Monoporeia affinis and Pallaseopsis quadrispinosa, and mysid Mysis relicta, and models their abundance as a function of environmental variables and the presence of invasive Ponto-Caspian mysids and amphipods. 3. Our results revealed that M. affinis is likely extinct in the country, whereas M. relicta was found in only 9 out of 16 locations from which it was previously recorded. The distribution of P. quadrispinosa appears to be shrinking. 4. Lake depth and water flowthrough intensity were significantly and positively associated with the relative abundance of relict mysids and amphipods, but no association was found with lake size or the presence of invasive Ponto-Caspian crustaceans. 5. We conclude that urgent action to mitigate the effects of nutrient run-off is needed to improve the status of glacial relict and other species that require good water quality. We also propose the re-introduction of glacial relict species in Lake Druksiai, where they went extinct during the operation of the Ignalina nuclear power plant that heated the lake, but where deep-water environmental conditions have improved following the powerplant closure in 2010.