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The European Habitats Directive was adopted to halt the rapid loss of biodiversity and has become an important instrument for protecting biodiversity in the European Union. Three aquatic plant species protected under the European Habitats Directive have so far been found in Lithuania: Aldrovanda vesiculosa, Caldesia parnassifolia, and Najas flexilis. Our aim in this study was to evaluate the former and current distribution and the status of conservation of the target species. Screening for the above-mentioned protected aquatic plant species was performed in 73 natural lakes throughout Lithuania in 2019–2021. We confirmed extant populations of Aldrovanda vesiculosa in four lakes, Caldesia parnassifolia in two lakes, and Najas flexilis in four lakes in the northeastern part of the country. We studied Aldrovanda vesiculosa populations three times (2015, 2019, and 2022) in Lake Rūžas and once each in Lake Apvardai and Lake Dysnai (2020). The population density of Aldrovanda vesiculosa ranged from 193.4 ± 159.7 to 224.0 ± 211.0 individuals/m2, the mean length of plants ranged from 12.5 ± 2.1 to 14.3 ± 2.7 cm, and the mean number of apices ranged from 2.0 ± 0.7 to 2.2 ± 0.9 per individual. The habitat of Aldrovanda vesiculosa in Lake Rūžas covered an area of about 3 ha. The number of generative individuals of Caldesia parnassifolia widely varied between years in Lake Rūžas. All populations of Najas flexilis were small, although the potential habitats in the studied lakes cover relatively large areas. We propose designating all lakes with populations of Aldrovanda vesiculosa, Caldesia parnassifolia, and Najas flexilis as special areas of conservation, as well as developing and implementing action plans for the conservation of these species and their habitats.