Twenty species of fish inhabit the Krka River, the most common of which are the Illyrian ide (Leuciscus illyricus), Dalmatian rudd (Scardinius erythrophthalamus hesperidicus) and brook trout (Salmo trutta m. fario).
The upper course of the Krka, upstream from Roški slap waterfall is characterised by its cold, fast waters, dominated by trout. The lower course, downstream from Roški slap, is lake-like and dominated by cyprinids. There are ten fish species that are endemic to the Adriatic river basins: Adriatic salmon, huchen, Adriatic dace, Dalmatian rudd, Croatian dace, Dalmatian barbel gudgeon, Adriatic barbel, Illyric ide, Visovac goby and the Dalmatian minnow. The wealth of endemic species is owing to the geological history of the area, and makes the Krka River a natural monument of the highest category.
The lake-like parts of the upper course, reeds, marshy meadows and ponds are abundant in amphibians, while rocky terrain with scarce vegetation are habitats for reptiles. To date, 9 species of amphibians (Amphibia) and 22 species of reptiles have been recorded in the park area. All these species are protected in Croatia, while the Red Book of Amphibians and Reptiles of Croatia includes the following: an endangered species is the loggerhead sea turtle (Caretta caretta); a vulnerable species is the olm (Proteus anguinus), the largest subterranean animal and endemic to the Dinarid karst, which inhabits four caves within the park boundaries; data deficient species are the smooth newt (Lissotriton vulgaris), which is found in the ponds in the northern part of the park, the leopard snake (Zamenis situla ) and the dice snake (Natrix tessellata); near threatened species are the common tree frog (Hyla arborea), a true acrobat in the world of the amphibians, as it can hang from one leg from a tree branch, or stand horizontally against a carob lea, the Italian wall lizard (Podarcis sicula), Hermann's tortoise (Testudo hermanni) and the European pond terrapin (Emys orbicularis). The loggerhead sea turtle only occasionally enters the brackish waters near Skradin, while the terrestrial turtles and pond terrapins are found throughout the national park. The Italian wall lizard is found in all habitats, from the marshy meadows to the dry rocky fields, and is the most common lizard species in the park. The dice snake inhabits the calmer aquatic habitats, while the leopard snake inhabits the thickets and rocky areas.
The only venomous snake found in the park is the nose-horned viper (Vipera ammodytes), which is a danger to man. There are also two semi-venomous snake species: the Eastern Montpellier's snake (Malpolon monspessulanus) and the European cat snake (Telescopus fallax). Their venom is dangerous only to reptiles, birds and small mammals.
To date, 211 bird species have been recorded in Krka National Park, and of these 111 species are listed as threatened in Croatia. The national park is a nesting site for 105 species, a resting or feeding site for 90 migratory bird species, and a wintering ground for 61 species, thus making the Krka area an important international area for migratory birds. There are 9 endangered species (7 nesting species and 2 wintering species) found in the park, whose local populations account for more than 1% of the total national population. These are: pygmy cormorant (Phalacrocorax pygmaeus), Eurasian bittern (Botaurus stellaris), golden eagle (Aquila chrysaetos), Bonelli's eagle (Hieraaetus fasciatus), peregrine falcon (Falco peregrinus), merlin (Falco columbarius), little crake (Porzana parva), spotted crake (Porzana porzana) and calandra lark (Melanocorypha calandra).
Ornithologically interesting areas in the national park are: Skradinski buk and its reeds, and the areas both upstream and downstream, the mouth of the Čikola River with Torak Lake, the canyon sections of the Čikola River, Visovac Lake and Roški slap. These localities best show the diversity and wealth of bird fauna, with typical representatives of nesting birds, migratory birds and wintering birds in each habitat type. At Roški slap, one can observe cliff species and wetland species together in a small area, while at Skradinski buk, one can view wetland species and the birds of the Aleppo pine forests and submediterranean rocky habitats.
A total of 46 species of mammals has been recorded in Krka National Park. Of these, 14 species have been included in the Red Book of Mammals of Croatia: in the category of regionally extinct is Mehely's horseshoe bat (Rhinolophus mehely); endangered species include the long-fingered bat (Myotis capaccinii) and Schreiber's bat (Miniopterus schreibersii); vulnerable species include the Mediterranean horseshoe bat (Rhinolophus euryale), Blasius' horseshoe bat (Rhinolophus blasii), Bechstein's bat (Myotis bechsteinii); near threatened species include the otter (Lutra lutra) and greater horseshoe bat (Rhinolophus ferrumequinum), lesser horseshoe bat (Rhinolophus hipposideros), Geoffrey's bat (Myotis emarginatus), greater mouse-eared bat (Myotis myotis), red squirrel (Sciurus vulgaris), garden dormouse (Eliomys quercinus) and the wolf (Canis lupus). Four species on the European endangered species list can be found in Krka National Park: greater horseshoe bat, wolf, otter and wild cat (Felis sylvestris).