In the wet season, Magpie Geese form large colonies whose honking sounds carry across the water.

Floating nests are constructed and the birds mate - one male and one or two females. By the middle of the wet season, the males are incubating 4-15 (but typically 8) eggs. The males raise the young and must remain near the nests. Seeds of Wild Rice (Oryza meridionalis) are important food for the adults and rapidly-growing hatchlings but, because of the large colonies, food is in short supply near the nests by the end of the nesting season and the birds are in poor condition for lack of food.

Late in the wet season, when the young birds can fly, the Magpie Geese migrate to permanent waters where they spend the dry season. The Bulkuru sedge or Water Chestnut (Eleocharis dulcis) becomes important, the Magpie Geese digging their faces into the mud and using their hooked beaks to extract the starch-rich corms (underground parts of the stem); the heavy face-plate protects the birds in this activity.

With the first rains of the next wet season, food availability increases rapidly and the birds' condition improves, in preparation for the next breeding season.

Magpie geese are long-lived, with lifespans of up to 30 years. The species was first described from the Hawkesbury River (NSW) by famed English ornithologist, John Latham, who gave it the species name 'semipalmata', referring to the feet, which are only partially webbed.

Once abundant across Australia, drainage of swampy grassland habitats in southern Australia a century ago now sees large colonies only in northern Australia, with populations in Kakadu National Park reaching about 500 000. The habitat of northern populations is threatened by environmental weeds including the escaped pasture plant, Para Grass (Brachiaria mutica), and the Giant Sensitive Plant (Mimosa pigra).

Indigenous people hunt Magpie Geese by various means: throwing sticks, from underwater using hollow reeds as snorkels or stalking and hand-catching. They are prized food and are usually roasted; the eggs are also eaten. Although protected from non-indigenous hunters in most of Australia, the Magpie Goose is a declared game species in the Northern Territory.