Due to intensive agriculture, particularly polderised areas, vegetation diversity and abundance of species in the Nemunas delta is not large. Nevertheless, 15 Lithuanian Red book species are recorded in the park territory. The two species (Allium Nymphoides peltata and angulosum) is at the extinction. Another 10 species are classified as category II in the Red Book (rapidly vanishing species) and 2 - category III. 6 found in the park there are rare plant communities (contender in the plant communities of the Red Book).
The Nemunas. During flood periods there settles a number of alluvial deposits along the main branches of the . As a result, in places (in Galzdonai andNemunas River Ragininkų section) there emerged a narrow band with a unique in Lithuania dunes, which lies on the meadows where growing rare Red Book species and communities. The largest delta is made up of ecological bar with a high ground water level, a siltation marsh soil, which increases hydro mesospheric grassland and wetland species and communities.