The greatest human impact in Southwest Australia has been the clearing of native vegetation for agriculture. Agricultural development began in 1829, with the arrival of the first European settlers to the region. However, because of the poor soils, development progressed slowly until the 1890s, when phosphate fertilizers were introduced. Today, most usable private land in the region is farmed, although it requires the application of phosphate, as well as zinc, copper, cobalt, and molybdenum. Because of the region's long dry seasons, bush fires have traditionally been used for hunting and clearing land. Although native plants are highly adapted to fire, the alteration or intensification of burning regimes can dramatically change the composition and condition of the natural vegetation.
One of the most serious current threats to the natural vegetation of Southwest Australia is the spread of root disease, or "jarrah dieback" caused by the root fungus Phytophthora cinnamomi. The disease was first noticed in the jarrah forests in 1940 but not identified until 1965. By that time, thousands of hectares of forest had been infected and killed. Root disease is now spreading to other habitats, including kwongan shrublands, and in particular Stirling Range National Park, where it has caused mortality among susceptible plants like the grass trees (Xanthorrhoea spp.) and members of the Proteaceae, especially the Banksias.
Large-scale mining for bauxite is increasingly a threat to Southwest Australia's ecosystems; the region is one of the largest producers of alumina in the world. Open-pit mining destroys habitats and pollutes waterways. However, recent reclamation efforts have been successful at establishing native plants in abandoned mine pits, a technique that holds promise for land management in the region.
Introduced alien species, especially foxes and cats, threaten native fauna and have caused major declines in species like the numbat in Southwest Australia. Land managers have successfully poisoned these alien species with sodium flouroacetate; amazingly, native mammals are immune to the poison because the compound occurs naturally in the leaves of many native legumes.
Today, of the principal vegetation types found in the region, 89 percent of the Eucalyptus woodlands have been lost, while 50 percent of the Eucalypt-dominated mallee and 59 percent of the Kwongan heath formations have been cleared. In total, only 30 percent of the original vegetation remains in more or less pristine condition.