A Daly River tourism operator has spoken out against the cotton industry, saying he is concerned about its potential impacts on the river and its barramundi population.
However, NT Farmers claims rules and regulations in place would mean barramundi stocks will not be at risk from cotton farming.
Daly River Fishing Retreat Owner Harold Sinclair said he is concerned about what the demand for water from Agribusiness companies, including for proposed cotton gins in the Katherine region, will do to the river systems.
"Many of us have concerns about the increasing demands for water access from large Agribusiness companies seeking to expand operations in the Daly catchment," he said.
"We are proud hard working business people, we're creating jobs, and we know what is sustainable here at the Daly."
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Mr Sinclair said he is concerned an increased demand for water will diminish the river's barramundi population, and therefore, have a detrimental impact on the local tourism industry.
"Tourists from far and wide travel to the NT to try and catch one of the Daly's legendary Barramundi and explore one of the most beautiful and healthy rivers in Northern Australia," he said.
"Fishing tournaments held here inject many dollars into the NT economy and significantly boost the Territory's tourism brand. Business owners like myself have financially invested in developing and growing the infrastructure with a long term operational business plan based on Barramundi fishing."
Marine Ecologist for Territory Rivers: Keep 'em Flowing Jason Fowler said Barramundi stocks in the Daly River rely on flood waters, which he said would be "harvested" by cotton farms.
"It's very easy to envision that good fishing on Daly River will become less and less," he said.
Mr Fowler said the NT is at risk of some of the problems faced by the Murray-Darling Basin, including the death of thousands of native fish.
"The Territory rivers are more at risk than the Murray Darling. We have the longest dry season in the world," he said.
"The rainy period is when they (the cotton industry) want to capture the flood waters."
NT Farmers CEO Paul Burke said cotton farming was supported by "extensive guidelines" that would prevent detrimental impacts to nearby river systems.
"NT Farmers would welcome scientific studies to substantiate claims that barramundi populations will be impacted by cotton production in the region. It should be noted that despite years of agricultural production in the region, our river systems are in a healthy condition," he said.
"Strict limits are in place to ensure that chemical run off and spray drift is prevented whenever additional inputs are applied."
Mr Burke said maintaining the health of the rivers was also in the best interests of farmers, including cotton farmers.
"It is important to emphasise that growers depend on healthy river systems for their businesses and lifestyles. Growers have an interest to maintain healthy rivers, many farmers enjoy fishing on the Daly whenever they get the chance."
He also labelled the comparison between the NT and the Murray-Darling Basin as "deceptive and misleading"
"The two regions have completely different histories, regulations and climatic conditions. Poor regulation damaged the Darling, decades of government mismanagement and inadequate oversight resulted in the situation that the river is in today," Mr Burke said.
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