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.
The major threat to Wilson Inlet is eutrophication, with the nutrient enrichment originating from a range of sources in rural and urban areas. The main source is considered to come from fertiliser application to pastures and crops as well as intensive animal production farms. There are a range of other developmental and environmental pressures on Wilson Inlet, its foreshore and its catchment arising from coastal development, weeds, use of pesticides in agriculture and plantation forestry, etc. Ruppia megacarpa is the main underwater flowering plant in Wilson Inlet. This seaweed is considered by some as a nuisance and by others, including scientists, as a vital part of the estuarine ecosystem, including as an important habitat and nursery for fish. The Inlet is of regional and state wide significance, and has been intensively studied by scientists over the past 15 years.