But cotton growers are calling the report 'a work of fiction'.

The report, A Fork in the River - the consequences of a major new cotton industry in the Northern Territory, recommends a ban on large-scale flood water extraction across the NT and a moratorium on new water allocations in the Roper River and Daly River catchments, in a bid to protect Top End rivers.

Report author the Centre for Conservation Geography's Carol Booth said Australia's cotton industry's major ambitions in the Northern Territory would project 'a future of hundreds of thousands of hectares of cropping, watered by billions of litres of water extracted from aquifers, rivers and floodplains'.

"The NT has an opportunity to learn from and avoid repeating the mistakes so evident in the Murray Darling Basin," Ms Booth said.

"But the cotton industry is ignoring numerous government and scientific studies on the environmental constraints to cropping in the north and downplaying the potential for major environmental, cultural and economic impacts."

The report's release comes as the NT Government is finalising its strategic water plan - due to be released this year - which will guide water management and policy until 2050.

But the peak industry body representing and advocating for plant-based industries in the Northern Territory, the NT Farmers Association, said it was disappointing that 'the authors of the document did not consult with industry to better understand the industry and its future vision'.

"The document makes assumptions that are not supported by the actual growth and development of the cotton sector in the north," NT Farmers CEO Paul Burke said.

"The document makes assertions regarding the volumes of water that the industry intends to use, when what has been experienced on the ground has in-fact been the opposite."

Mr Burke said the authors 'failed to contact any actual cotton growers', or organisations that have been 'fundamental in the development of the broadacre industry'.

"It should also be considered that this document does not seek to understand the economic opportunities that responsible agriculture development can create to support regional and remote communities.

"Territorian are already experiencing job opportunities from the regional development being undertaken.

"This development will also continue to build the case for greater investments in local infrastructure."

A local cotton grower, who did not want to be named, called the report 'a work of fiction'.

"Even nearly all its illustrations are from somewhere other than the NT," the grower said.

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NT Environment Centre co-director Kirsty Howey said the NT's water management and planning frameworks were 'widely acknowledged as deficient' and water reforms were 'sorely required'.

"We've seen the area subject to land clearing approvals rapidly accelerate in the NT by 300 per cent over the past four years, with proposals for cotton cropping expected to require much more," she said.

"If we are to avoid the mistakes caused by over-allocation and intensive irrigation in the Murray Darling Basin, we need a different approach here in the Territory - one that looks at basin-wide management.

"Water policy needs to support local economies, not enable big business to take more water from already stressed systems."

The report recommends the Northern Territory Government places a moratorium on new water licences and allocations and cap extractions at current levels in the Daly and Roper river catchments.

It also suggests prohibiting large-scale extraction of flood waters in the Northern Territory and integrated catchment planning with a priority focus on maintaining the health of NT's rivers and protecting their environmental values.

"In recognition of the limited science to inform decisions about large-scale cotton farming, apply the precautionary principle in a meaningful way to prevent irreversible harm," the report suggests.