The Krka River area abounds in various types of subterranean habitats that are inhabited or are shelter for rare and threatened animal species. The list of subterranean fauna contains about 90 terrestrial and aquatic animal species.
More than half of the recorded species are endemic to Croatia and the Dinarid mountain region, while the freshwater cave snails (Dalmatella sketi and Lanzaia skradinensis), cave pseudoscorpions of the genus Chthonius and the cave isopod of the genus Calconiscellus are endemic to the Krka National Park area. Exceptional finds includes those of the endemic freshwater cave polychaete (Marifugia cavatica), a Pliocene relict, and the endemic amphibian olm (Proteus anguinus), first discovered in the park in 1989. Nine bat species take shelter in the caves, and of these, eight species are threatened and included in the Red Book of Mammals of Croatia.
One of the largest bat colonies is that of the long-fingered bat (Myotis capaccinii). Among other animal species, the largest isopod in Croatia is found here, the endemic Dalmatian cave cricket (Dolichopoda araneiformis).