Wet, intermittently flooded freshwater coastal and shallow water habitats are notable for their high biodiversity. Many of the usually semiaquatic annuals or small perennials common in such habitats are in decline due to the high sensitivity of such habitats to changes caused by anthropogenic and natural factors. The Euro-Siberian semiaquatic Elatine hydropiper rarely occurs in Lithuania and is protected there and in other Baltic and Central European countries. In 2020, we found a large population of Elatine hydropiper in southern Lithuania (Varėna district) in Lake Pabezninkai and its exposed shores. The water level of the lake has receded by about 1.5-1.6 m since 2018, exposing wide, wet, and sandy or silty shores. The aim of this study was to determine the status of the Elatine hydropiper population and to assess its potential for long-term survival. The objectives of the study were to (a) determine the size and quantitative characteristics of the population, (b) assess the seed bank in the shallows and exposed shores of the lake, (c) assess the species diversity in the communities with Elatine hydropiper, (d) evaluate the conservation value of the studied species and the lake habitat. The studies were carried out between 2020 and 2021. The number and coverage of plant patches as well as seed bank studies were carried out at three sites with different shoreline substrate. At each site, the number of patches and coverage was assessed in 50 sample plots of 100 cm2. The seed bank was examined in the top 5 cm of the substrate. A total of 90 substrate samples were analyzed. We found that Elatine hydropiper grows on ca. 0.38 ha in the lake and on ca. 0.95 ha on the shores. On the exposed shores, the mean number of Elatine hydropiper patches per 1 m2 was 2155 ± 1241.5 and their mean cover was 23.17% of the surface. Seed bank analyses revealed that the seeds and seed shells were significantly more abundant in the bottom sediments than in the shore sand or silt. The mean number of seeds per liter of soil was 85.8 ± 210.2, and the mean number of seed shells was 217.0 ± 265.8. The assessment of the status of the species in Lithuania according to the IUCN (International Union for Conservation of Nature) criteria has led us to conclude that it should now be classified as vulnerable [A3; B1ab(iii); C2a(ii); D2]. The key to protecting Elatine hydropiper and other co-occurring rare species with similar ecological and biological characteristics, as well as the plant communities of shallows and exposed wet banks, is to protect their habitats. The survival of the species and their habitats could be assured by recurring significant water level fluctuations in the lake, resulting in periodic emergence of patches of wet sand or silt free from perennial vegetation.