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The Basin is home to hundreds of species of native animals. The rivers and surrounding environments support many fish, birds, mammals, reptiles, amphibians and insects.

The number of species of native animals, as well as the population and spread of communities of each species, is an indicator of the health of the ecosystems of the Basin. Each type of native animal or group of animals has a role to play in its ecosystem. Carnivores keep other animals from becoming too numerous, and herbivores manage vegetation growth and recycle organic matter.

Native animals also provide an economic benefit to Basin communities by bringing tourists to the regions — they are also enjoyed by locals.

State governments, through their natural resource agencies, work to protect native animals by managing habitat loss, disruption and fragmentation, and by controlling feral animals.

The Basin is home to:

  • 367 species of birds (35 endangered), which include 98 species of waterbirds
  • 85 species of mammals (20 extinct, 16 endangered)
  • 46 species of native fish
  • 53 species of native frogs
  • 46 species of snakes (5 endangered)
  • 100 species of lizards (1 endangered)
  • 3 species of freshwater turtles
  • 124 families of macroinvertebrates.

Many of the native plants and animals in the Basin are protected in national parks and other reserves, which comprise about 7% of the Basin's total area. Despite significant efforts to conserve remaining populations, at least 20 mammal species which lived in the Basin have become extinct since European settlement.

During the past 150 years,  native fish populations in the Basin have fallen significantly and their distribution has contracted. This is largely due to habitat loss or modification, barriers to fish movement, and the impacts of alien species. The decline of native fish populations is a warning that the natural ecological function of the rivers is at risk.