More than 300 bird species have been observed in the Lake Kerkini National Park. 137 of these species nest, 134 overwinter and 163 use the wetland and the surrounding area as an intermediate resting and foraging stop in their migration routes.

A total of 10 species nest in mixed colonies in the riparian forest, which is a significant number both for Greek and European standards. These species are: the great cormorant (Phalacrocorax carbo), the little egret (Egretta garzetta), the great white egret (occasionally) (Egretta alba), the purple heron (Ardea purpurea), the grey heron (Ardea cinerea), the squacco heron (Ardeola ralloides), the night heron (Nycticorax nycticorax), the spoonbill (Platalea leucorodia), the pygmy cormorant (Phalacrocorax pygmaeus), the glossy ibis (now occasionally) (Plegadis falcinellus). In floating nests, in the riparian forest and the remaining reedbeds breeds the great crested grebe (Podiceps cristatus), the little grebe (Tachybaptus ruficollis), the black-necked grebe (Podiceps nigricollis), the coot (Fulica atra) and the common moorhen (Gallinula chloropus), as well as the swan (Cygnus olor) since 2009, while the whiskered tern (Clidonias hybridus) and the black tern (Chlidonias niger) nest in the leaves of lilies or other aquatic plants. Other important species breeding in the area are: the black stork (Ciconia nigra), the white stork (Ciconia ciconia), the peregrine falcon (Falco peregrinus), the short-toed eagle (Circaaetus gallicus), the lesser spotted eagle (Aquila pomarina), the white-tailed eagle (Haliaaetus albicilla) and the booted eagle (Aquila pennata).

Many thousands of waterfowl overwinter in the lake. Moreover, the presence of rare birds of prey is also remarkable, for example the imperial eagle (Aquila heliaca), the golden eagle (Aquila chrysaetos), the peregrine falcon (Falco peregrinus), the greater spotted eagle (Aquila clanga) and the white-tailed eagle (Halliaaetus albicilla). Over the last years, new species have also been observed in the area, either during migration or in winter, such as the white-headed duck (Oxyura leucocephala), the saker falcon (Falco cherrug), the flamingo (Phoenicopterus roseus), the Tundra swan (Cygnus columbianus), the goosander (Mergus merganser), the lesser white-fronted goose (Anser erythropus) etc. Lake Kerkini (along with the area of Porto Lagos) is the most important wintering area for Dalmatian pelican (Pelecanus crispus) throughout Europe.

There are also many species of mammals. The otter (Lutra lutra) is met in the lake, in channels and ditches. The red fox (Vulpes vulpes), the wildcat (Felis sylvestris), the least weasel (Mustela nivalis), the European polecat (Mustela putorius), the beech marten (Martes foina) are met in the wetland and the surrounding mountains. The grey wolf (Canis lupus) is met in the wetland at specific times of the year, while it is mostly found in the surrounding mountains, where there are also wild boars (Sus scrofa) and roe deer (Capreolus capreolus), whereas golden jackals (Canis aureus) are mainly met in the north, east and southwest part in small numbers.

The area of the lake hosts the largest number of water buffalo in Greece, a species that is under the protection of the Greek state. In the past, water buffalo could be found in most of wetlands of Macedonia, Thrace and Thessaly but in the last 50 years they have been restricted to only a few wetlands in the country.

In the lake, as well as in river Strymonas downstream of the lake, 32 fish species have been recorded. The most important of them are: the common carp (Cyprinus carpio), the crussian carp (Carassius gibelio), the bleak (Alburnus alburnus strumicae), the chub (Squalius orpheus), the roach (Rutilus rutilus), the Macedonian vimba (Vimba melanops) and the barbel (Barbus strumicae), while the eel (Anguilla anguilla) has disappeared from the lake since the the new dam came into operation. Among these, there are also certain alien species, which obviously came to the lake from Bulgaria in the Strymonas. With regard to these species, the population of pumpkinseed sunfish (Lepomis gibosus) was on the rise in the 90s, but then withdrew and now is balanced, while Gymnocephalus cernuus, whose natural distribution is in central and north Europe, appeared in fishermen nets in 2009-2010 with a growing presence since.

The reptiles are represented in the area by at least 25 species, the most characteristic of which are: the Balkan pond turtle (Mauremys rivulata), the European legless lizard (Pseudopus apodus), the javelin sand boa (Eryx jaculus) and the grass snake (Natrix natrix). The amphibians are represented by at least 11 species including the Eastern spadefoot (Pelobates syriacus) and salamander (Salamandra salamandra).

Concerning invertebrates, there are at least 4,700 species, more than 1,396 of which are new species for Greece and at least 46 are new species for science, which means that until now they have been recorded only in the Lake Kerkini National Park and nowhere else in the world.