Abstract Glacial relict crustaceans are characterized by their affinity for cold and well‐oxygenated waters and their limited dispersal ability. They occur in large, deep lakes of Northern and Central Europe and North America, with their distributions shaped by glaciation events. In many countries and especially along the southern distribution edge, glacial relict populations are declining as a result of eutrophication, global warming, and possible adverse interactions with invasive Ponto‐Caspian crustaceans. This study assessed the status of three glacial relict malacostracan species (the amphipods Monoporeia affinis and Pallaseopsis quadrispinosa and the mysid Mysis relicta) in Lithuania and modelled their abundance across environmental variables, including the presence of Ponto‐Caspian malacostracans. The results showed that M. affinis is probably extinct in the country, whereas M. relicta was found in only nine out of 16 locations from which it was previously recorded. The distribution of P. quadrispinosa also seems to be shrinking. The annual water renewal rate (P. quadrispinosa and M. relicta) and lake depth (P. quadrispinosa) were significantly and positively associated with the relative abundance of relict mysids and amphipods, but no association was found with lake size or with the presence of invasive Ponto‐Caspian crustaceans. Both species were less abundant in samples collected in the 21st century compared with the 20th century. Given the biogeographical and ecological importance of glacial relict crustaceans, their widespread declines are of concern and point to the deterioration of habitat quality, essential for other species with similar requirements. Urgent action is needed to improve water conditions and safeguard these communities. In cases where water quality improves, the reintroduction of extirpated relict populations should be considered. One example is Lake Drūkšiai, where these crustaceans became extinct during the operation of the Ignalina nuclear power plant but where conditions improved following the closure of the power plant in 2009.