The NT government should ban large-scale floodwater extraction and prohibit new water licences in the Roper River and Daly River catchments, according to A Fork in the River.
"Australia's cotton industry has major ambitions in the NT, projecting a future of hundreds of thousands of hectares of cropping, watered by billions of litres of water extracted from aquifers, rivers and flood plains," the reports author, Carol Booth from the Centre for Conservation Geography, said on Tuesday.
"The NT has an opportunity to learn from and avoid repeating the mistakes so evident in the Murray Darling Basin."
Dr Booth said the cotton industry was ignoring government and scientific studies on the environmental constraints of cropping in northern Australia.
NT Environment Centre director Kirsty Howey said the NT's water management and planning frameworks were too weak.
"Our water management laws have not incorporated reforms agreed to under the 2004 National Water Initiative," she said.
Ms Howey said land clearing approvals had increased by 300 per cent during the past four years, and the cotton industry could require much more.
NT Farmers forecast in 2019 that 77,000 hectares of land would be used for cotton cropping by 2029, which is a 4000 per cent increase in less than a decade.
"We need a different approach here in the territory," Ms Howey said.
"Catchment planning should be driven by community desires to protect rivers, especially those of traditional owners."
Global public policy advocates, Pew Charitable Trusts, says the NT has some of the planet's last tropical free-flowing rivers.
"Our rivers and floodwaters sustain diverse and rare ecosystems and wildlife, such as the critically endangered Largetooth Sawfish and the endangered Pig-nosed Turtle," manager Mitch Hart said.
Large-scale cotton growing could impact these and important fisheries, such as barramundi and prawns.
"Recreational fishing contributes an estimated $26 million each year to the NT economy, with 80 per cent of that coming from interstate or overseas visitors," Mr Hart said.
The report made six recommendations to the NT government, including for it to undertake integrated catchment planning with a priority focus on maintaining the health of the NT's rivers.
Its release comes as the NT government works to complete its draft strategic water plan, which is set to be completed by 2023 and guide the territory's water management and policy until 2050.
The report A Fork in the River was commissioned by the Territory Rivers group, which is an alliance of scientists, local communities and non-government organisations, including The Pew Charitable Trusts and the Environment Centre NT.
Cotton Australia has been contacted for comment.
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