The biodiversity of the aquatic ecosystems is exceptionally valuable. Three very important Natura 2000 habitats types are represented in the aquatic ecosystems of the national park: Hard oligo-mesotrophic water with benthic Chara vegetation (Characeae) (3140), Watercourses with vegetation Ranunculion fluitantis and Callitricho-Batrachion (3260), and Tufa cascades of karst rivers of the Dinaric Arc (32A0).
Habitat type 3260 also often encompasses the Natura target plant species, creeping marshwort Apium repens, which grows in wet and aquatic habitats such as wet meadows, ditches, shallow ponds, and river backwaters. Other Natura species associated with aquatic habitats found in the park include: ornate bluete Coenagrion ornatum, stone crayfish Austropotamobius torrentium, kingfisher Alcedo atthis, long-fingered bat Myotis capaccinii and river otter Lutra lutra. All these species require good water quality, and their presence indicates the good quality and conservation of these aquatic habitats. In addition to the target Natura species, these aquatic habitats are home to many other interesting, important, indicator species, and endemic, threatened and strictly protected species, such as numerous species of diatoms, algae and mosses, caddisflies (Trichoptera), dragonflies (Odonata), stoneflies (Plecoptera), European crayfish Astacus astacus, brook trout Salmo trutta, alpine salamander Salamandra atra, Italian crested newt Triturus carnifex and white-throated dipper Cinclus cinclus.
Other important habitats are the wetland localities, such as the shoreline of Liman draga, the backwaters of Prošćansko jezero Lake, the branches of the Bijele Rijeke (White River), the reservoir on Bijela Rijeka (White River), localities along the Matica River, and more.