Cotton has become a contentious crop in this drought.

Farmer Andrew Watson, from Boggabri in north-west New South Wales, says some of the criticism of irrigators has been vicious.

"Having seen some death threats … it just shows there's a real lack of understanding of how the systems work," he said.

"We only use the water that's allocated to us."

It's harvest time and Mr Watson says this year's crop is down.

"We've actually had a real shortfall in water. So the crop outcome is not very good," he said.

"We're probably going to produce an outcome that's about 70 per cent of what we'd like to produce."

Unless there's significant rain, next year will be worse.

Mr Watson says this year's cotton harvest has only been possible by using bore water. ( ABC News: Jessie Davies )

All but dry

Bore water allocations have been a saviour on this farm.

"My overall business water entitlements are made up of about 50 per cent river water and 50 per cent bore water," Mr Watson said.

"This year we've only probably had about 10 per cent of our river water entitlement, which has been saved from water allocations made in 2016."

But that water came from the last flow down the Namoi River, released from Keepit Dam. And both are now all but dry.

Cotton farmers on the Namoi River have harvested a crop using mostly bore water. ( ABC News: Ben Deacon )

Despite having zero water allocations this year, irrigators like Mr Watson were able to use some of that water because they carefully saved it from previous allocations.

"We chose to save that bit of water," he said.

"I find it a bit unfair that when it gets a bit tight, people want to take that back off us again."

Water authorities say that when allocating water, they prioritise people, stock and the environment ahead of irrigators.

Bitter taste

Either way, the water is now gone and everyone is upset about it.

Downstream at Walgett, where the end of the Namoi joins the Barwon River, the town has been on an emergency supply of bore water.

It's deemed safe by health authorities but it's high in sodium. Many say it's unpleasant to drink, and could have implications for people with kidney or heart conditions.

The Namoi River stopped flowing at the end of last year. ( ABC News: Jessie Davies )

Local Gamilaraay elder Clem Dodd said the lack of river water was making people miserable, not just because people couldn't drink it but also because people could no longer swim or fish.

"I remember we used to spear fish and all in this, it was clear," he said.

He said the water resources should have been managed better.

"It's just terrible, it shouldn't be like this," he said.

Devastated by drought

The Namoi River runs for 700km through the northern basin of the Murray-Darling system. ( ABC News: Jessie Davies )

But water managers say it's the lack of rainfall that's to blame.

Adrian Langdon from Water NSW said it was one of the worst dry periods on record for the region.

"The Namoi system is probably one of the most devastated systems by the drought," he said.

Mr Langdon said that without irrigators storing water in Keepit Dam, the river would have run dry much sooner.

"Because of the releases from Keepit Dam over the last two years, the flow in the system has been three times what would have occurred under natural events," he said.

"We've had ceased-to-flow conditions along the Namoi since December, when Keepit Dam was emptied."

That release was a "block release" for people, stock, the environment and then for irrigators, he said.

But draining the dam to less than 1 per cent of its capacity has also caused heartache upstream.

Keepit Dam is at less than 1 per cent capacity. ( ABC News: Ben Deacon )

'Tears in their eyes'

Annie Michie, from the Lake Keepit Family Fishing Club, was among those who advocated to keep more water in the dam through the drought.

"It's broken a lot of people in the area around here," she said.

"[We] had grown men standing on the banks, tears in their eyes, just watching this beautiful fishery die."

Ms Michie said she grew up on an irrigation property and was not anti-irrigation.

Anne Michie says the grim state of Keepit Dam and the Namoi River has been devastating for local communities. ( ABC News: Ben Deacon )

But she believed the way the water was allocated did not add up.

"The rules need to be changed," she said.

"Water managers are writing cheques they can't cash … There's over-allocation is what it simply comes down to."

But right now there's simply no water to allocate, unless it comes from underground.

And some ecological experts are warning that the Namoi system could be approaching a new low.

'Tipping point'

Professor Martin Thoms, from the University of New England in northern NSW, said there were warning signs.

"Indicators are suggesting that we're moving towards a major tipping point," he said.

"The thing is if we go over a tipping point into what I call a different type of river and different types of environment, you can't bring it back."

Professor Martin Thoms is an internationally recognised expert in riverine ecosystems. ( Supplied: Martin Thoms )

Professor Thoms said that in spite of all the argument over management of the Murray-Darling Basin, everyone wanted the same thing: a resilient system that could support all the life that depended on it.

"If we go over a major tipping point, all our data shows that you have lower productivity — lower productivity for the environment, lower productivity for the agricultural environment," he said.

"That means less money in the back pockets of regional and rural Australians."

He wants to see a greater focus on managing the environmental health of river systems, beyond just water flows.

Rivers under 'enormous stress'

Professor Fran Sheldon, from the Australian Rivers Institute at Queensland's Griffith University, said that while the rivers in the Murray-Darling region did naturally stop flowing in dry times, they were under enormous stress at the moment.

"I think all of the rivers in the northern part of the Murray-Darling Basin could be potentially approaching tipping points," she said.

"We see globally where water is removed from systems it sends them closer and closer to these threshold points where they then change and they don't recover."

Fran Sheldon is a professor at the Australian Rivers Institute, Griffith University. ( Supplied: Fran Sheldon )

Professor Sheldon said the state of the river was caused by the drought, but water extraction was also playing a role.

She said when the drought did break, the first major flows down this river system needed to be protected to help the river recover.

"I do think the emergency management decisions would be to let first-flush flows through," she said.

Professor Sheldon said adaptive management was required while everyone waited to see what the Murray-Darling Basin Plan could deliver when more water returned to the system.

Water NSW said this was something that would be considered.

Grand plan

Mr Watson shows how cotton fibres can be drawn into a thread. ( ABC News: Jessie Davies )

The river did get a brief drink from recent rain, and that water was allowed to run its course uninterrupted.

Boggabri farmer Andrew Watson doesn't believe the river is at a tipping point.

He said it had been like this before and it would be like this again, and that there was little the Basin Plan or the state-based water-sharing plans could do to stop that.

"I don't believe that the Murray-Darling Basin Plan was ever intended to stop droughts. I don't think it can," he said.

"I think only God can do that."