Utilisation of water is often highly inefficient; especially the use of bore drains, where water is distributed from the bore head through open channels. Up to 95% of water is lost through evaporation and seepage. Bore drains encourage infestations of woody weeds like prickly acacia, and also provide habitat for feral animals. Bore drains can increase the concentration of minerals and salinity through evaporation.
Many of these problems can be overcome by replacing bore drains with poly pipe that is run out to stock troughs.
There are estimated to be over 3,300 free flowing bores in the basin, and 820 of these are bores are uncontrolled, usually flowing out into bore drains or wetlands, many artificial.
50 years ago pastoralists and governments becan installing headworks to control flows. This program continues today.
Draw down of water from the Great Artesian Basin has reduced water pressure in some of the naturally occurring springs reducing habitat and putting pressure on native flora and fauna.
From 1999 – 2009 the Australian government had committed 75 million dollars to accelerate repair work on wild bores and replace bore drains through the basin.
Some people argue that the traditional view of the geology of the basin is flawed and there is no natural recharge, and that bores are doing irrevocable damage.
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Because the basin underlies parts of Queensland, New South Wales, South Australia and the Northern Territory, which each operate under different legislative frameworks, policies and resource management approaches, the need for a coordinated "whole-of-Basin" approach to the management of this important natural resource resulted in the formation of the Great Artesian Basin Coordinating Committee (GABCC) which provides advice from community organisations and agencies to State, Territory and Australian Government Ministers on efficient, effective and sustainable whole-of-Basin resource management and to coordinate activity between stakeholders.
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