Zrmanja can be geographically defined as the south-east border of Velebit, and it is necessary to look at some animal species which found their habitat on this area of Velebit. Those are primarily dark and karst lizzards, karst mouse, a karst kind of garden doormouse, snow field-mouse and Dinara field-mouse, who are specialized for moving on rocks. The predators which feed with them are the horned viper and the owl. In higher areas of this part of Velebit you can find the gray doormouse, bears, wolves and the lynx.
A special habitat is the subterranean flow along which Zrmanja flows into Krka. Here, among cave water animals, there are endemic snails, water toads, and crayfish, and a population of the olm.
In the canyon part of Zrmanja, downstream from Žegar, Illirian iris and window bellflower. The green lizzard, which has a blue throut when mating, also inhabits this area.
Downstream from the mouth of Krupa into Zrmanja, under Visoki buk falls, out of the water rises a round and pointed rock. On this place, in the distant year 1863. a Croatian scientist Spiridon Brusina, discovered a certain snail species which is after him called Medora albescens brusinae. Zrmanja trout, Zrmanja dace, the Illyrian bullhead, the barbel, the white bleak, the minnow, the loach and others are among the 11 species of fish which inhabit this part of the river. There is also a white legged crayfish and the eel which manages to climb all the way upstream over all the falls. Beside the water blackbird, which hunts insects and their maggots, the otter, which is endangered, also is an inhabitant of this part of the river. The water here is also a habitat of endemic water snails Dalmatinella fluviatilis, Belgrandiela zermanica, islamia zermanica and Litoglyphulus tedanicus.
In the quiet part of the flow there are water-lilies, reed and cane. One of such areas is the lake HE Velebit where the American trout lives.
A good habitat is the part of Zrmanja from Jankovića buk to Novigrad sea, because along the bed there is a layer of sea water. Beside the bass, the flounder and the mullet, the sandsmelts come, and the endemic brackish goby lives here. There are many dice snakes, and with the pond turtle there are kingfishers, coots and wild ducks. In winter the shags and the small grebes are common; more infrequent is the Crested grebe. The bittern is uncommon, but in the warm part of the year, brackish water snails Hydrobia testadura, H. Salaria and Adriohidrobia concociella. In smaller springs near Obrovac, with other subterreanean snails, the endemic Hdziella sketi and Paladilhia illistris have been found. Mussels grow on the stony bottom right next to the bridge in Obrovac. During the day, the canyon walls resound to the song of blue rock thrush, and at night, along with the croaking of marsh frogs, you can hear the sound of the eagle owl setting off on its hunt for rodents and hares. The longfingered bats hunt for the true flies and caddflies over the surface of the water - today this species is a symbol of the protected karst rivers near the Mediterranean.
Beside owls you could hear the howling of jackals. The wolf recovered after it was protected, and unfortunatelly causes damage to local sheep farms. Wild boars also cause damage, and their number increased in the last 5-6 years.

As in case of fauna, the flora on the Zrmanja area is influenced by Mt Velebit. On the coastal rocks there is the window bellflower. Velebit's endemic species. There are no large forests in the area of Zrmanja and Krupa. Bare karst is covered by low bushes and thickets, and occasionaly few woods.
In thickets and woods, you can often find the pubescent oak and black hornbeam, beech and white hornbeam. The trees along Zrmanja are mostly ash-tree, black poplar and fig-trees, and near the water, poplars. On beaches along the river you can see the Illyrian iris and window bellflower, and pyramidal bellflower. On the stone plate of the canyon there are black poplars, broom, oaks, thorny bushes, juniper etc.
On meadows which are flooded during high waters, various sorts of clover grow, Trifolium resupinatum, Trifolium fragiferum and others.
Bushes of hawthorne and cornel often grow in this area. Along paths and roads you can often find plants like Chenopodium murale, Chenopodium vulvaria, sage, and many others.
The flora right next to the river is the water-lily, reed and cane.