The inlet supports a wide variety of fish: Sandy Sprat (Hyperlopus vittatus), Cobbler (Cnigoglnis macrocephalis), Pink Snapper (Chrysophrys auratus), Yellow-eye Mullet (Aldritechetta forsterri), Sea Mullet (Mugil cephalus) and Blue Mackerel (Scomber australasicus).
A large amount of waterbird species live in and at the Wilson Inlet: Australian Pelican (Pelecanus conspicillatus), Little Black Cormorant (Phalacrocorax sulcirostris) and Little Pied Cormorant (Phalacrocorax melanoleucus), Black Swan (Cygnus atratus), Grey Teal (Anas gibberifrons), Australian Shoveller (Anas rhynchotis), Blue Billed Duck (Oxyura australis), Red-necked Avocet (Recurvirostra novaehollandiae) and Silver Gull (Larus novaehollandiae).
The area surrounding the Wilson Inlet also supports many land bird, mammal and reptile species. Birds like Silvereye (Zosterops lateralis), Wetern Rosella (Platycerus icterotis), New Holland Honeyeater (Phylidonyris novaehollandiae), Tawny Frogmouth (Podargus strigoides), Port Lincon Ringneck (Barnardius zonarius), Purple Crowned Lorikeet (Glossopsitta porphyrocephala) and Red Capped Parrot (Purpureicephalus spurius) live here. Yellow Footed Antechinus (Antechinus flavipes), Honey Possum (Tarsipes rostratus) and Grey Bellies Dunnart (Sminthopsis griseoventer) are mammals, which live in the surrounding area of Wilson Inlet. Also reptiles like Spotted Brown Snake (Pseudodonaja affinis) and Eastern Tiger Snake (Notechis sscutatus) can be found here.