As part of the Rotoiti Nature Recovery Project native great spotted kiwi (Apteryx haastii) have been successfully brought back to Nelson Lakes. The project supports an area of 5000 ha protecting the local beech forest and its species from introduced predators such as stoats and possums.
Common native birds that are primarily found in lowland forest, waters and higher altitudes include:
Black shag (Phalacrocorax carbo), little shag (Phalacrocorax melanoleucos), black swan (Cygnus atratus), paradise shelduck (Tadorna variegata), grey duck (Anas superciliosa), New Zealand scaup (Aythyn novaeseelandiae), Australasian harrier (Circus approximans gouldi), New Zealand falcon (Falco novaeseelandiae), weka (Gallirallus australis), pukeko (Porphyrio porphyrio melanotus), spur-winged plover (Vanellus miles novaehollandiae), southern black-backed gull (Larus dominicanus), New Zealand pigeon (Hemiphaga novaeseelandiae), South Island kaka (Nestor meridionalis meridionalis), kea (Nestor notabilis), more pork (Ninox novaseelandiae), New Zealand kingfisher (Halcyon sancta vagans), South Island rifleman (Acanthisitta chloris chloris), New Zealand pipit (Anthus novaseelandiae), South Island fernbird (Bowdleria punctata punctata), brown creeper (Finschia novaeseelandiae), grey warbler (Gerygone igata), South Island fantail (Rhipidura fuliginosa fuliginosa), tomtit (Petroica macrocephala macrocephala), south island robin (Petroica australis australis), silvereye (Zosterops lateralis), bellbird (Anthornis melanura), tui (Prosthemadera novaeseelandiae), and yellowhammer (Emberiza citrinella).
Rare birds that have been significantly harmed through human settlement and introduced predators are:
Southern crested grebe (Podiceps cristatus australis), royal spoonbill (Platalea leucordia), blue duck (Hymenolaimus malacorhynchos), rock wren (Xenicus gilviventris), yellow-crowned parakeet (Cyanoramphus auriceps), and yellow head (Mohoua ochrocephala).
Due to the park's warm climate, the area of Nelson Lakes is a seasonal home for several migrating visitors such as:
Cattle egret (Bubulcus ibis), white-faced heron (Ardea novaehollandiae), white heron (Egretta alba), pied stilt (Himantopus himantopus leucocephalus), black-billed gull (Larus bulleri), black-fronted tern (Sterna albostriata), long-tailed cuckoo (Eudynamis taitensis), shining cuckoo (Chryrococcyx lucidus), and the welcome swallow (Hirundo tahitica neoxena).
Introduced bird species are also found here:
Canada Goose, mallard, California quail, skylark, song thrush, blackbird, chaffinch, sparrows, and starling.
The only native mammals found in New Zealand are bats of the Mystacinidae family. The lesser short-tailed bat (Mystacina tuberculata tuberculata) is known to live in southern parts of the South Island. However, populations exist in the northwest of Nelson Lakes National Park.
Introduced mammals are:
Red deer, chamois, cattle, wild pig, goat, brush tailed possum, hare, rabbit, rat, mouse, cat, ferret, weasel, and stoat.
Among the park's most famous insects is the giant carnivorous snail called Powelliphanta. The Powelliphanta is the largest land snail species on earth. Other famous insects include the fishing spider (Dolomedes dondalei) that is able to catch and poison smaller fish species. Common hazards are wasps, sandflies and bumblebees. Nelson Lakes is also known for plant lice that produce honeydew on trees, an important food source for several species in the park.
Lake Rotoiti and Lake Rotoroa are home to several freshwater species including the endemic long-fin eel (Anguilla dieffenbachii) as well as introduced brown trouts (Salmon trutta).