People in the lower Darling are up in arms after the NSW Government lifted an embargo on irrigators taking floodwater currently making its way down the river.

Key points: The three-day halt of the embargo will allow floodwater to be taken by some irrigatotrs in NSW

The three-day halt of the embargo will allow floodwater to be taken by some irrigatotrs in NSW Opponents of the move say allowing harvesting upsteam will prevent the floodwater reaching critical downstream locations

Opponents of the move say allowing harvesting upsteam will prevent the floodwater reaching critical downstream locations Queensland's cotton industry says it is comfortable with irrigators using their entitlements

The New South Wales State Government recently introduced an embargo on pumping from a tributary or harvesting floodwaters but that has been lifted for three days.

The Government said that flow targets had been met and floodwaters might cause damage to private infrastructure if irrigators could not divert it into dams.

The news has left graziers, indigenous groups and towns reliant on water further downstream feeling angered and confused.

Will water make it to Wilcannia?

Wayne Smith from Karoola Station, near Pooncarie in the Wentworth Shire is one of those.

"I'm a bit confused about what infrastructure could be damaged when it's all built to handle floods.

"It's not Noah's Ark type flooding, it's just the first flush and that's just a made up excuse, to put it mildly."

The change enables irrigators in some sections and tributaries of the Namoi, the Peel, the Gwydir and the Barwon rivers to pump or divert water for three days.

"A lot of water can disappear in three days," Mr Smith said.

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"We need some explanation for why it's been lifted, from us it just looks like greed."

The water could take six weeks to get to places downstream like Tilpa, Wilcannia and Menindee, but now that it can be pumped from places upstream it may not get there at all.

Flood plain harvesting impact unsure

Flood plain harvesting is different to other types of water extraction.

It refers to the interception of water flowing overland, before it gets into the river and often involves small levy banks or systems that divert water accumulated in low areas into water storages.

If irrigators can fill their dams it can provide water security for three to four seasons which would be an enormous boost for the farming businesses and regional communities that they contribute to economically.

It is not clear how much water is diverted by flood plain harvesting.

The NSW Government is investigating systems to regulate and account for it in the water sharing plans that govern water extraction.

Water take questioned

NSW Shadow water Minister Clayton Barr said the minister Melinda Pavey had backflipped on comments she made about Queensland irrigators taking water from the top of the basin.

He said a "massive" amount of water was taken in a flood.

"A great percentage of the run will never make it to the river because of flood plain harvesting."

"On every other day of the year these actions would have incurred a $2 million fine for a corporation or a $500,000 fine for an individual … and for three days the minister has said 'take what you want'," Mr Barr said.

Minister says 'infinitesimal' amount of water to be taken

The NSW Minister for Water, Melinda Pavey said the embargo was still in place for 99.9 per cent of the affected region and an "infinitesimal" amount of water will be taken on just a couple of properties.

She said the embargo was a historic first for the state, it would protect the water for the lower Darling and her department had taken a precautionary approach to the concerns of some irrigators.

The Natural Resource Access Regulator will be investigating those instances to make sure the correct decisions were made.

"Let's be fair to everybody, our first priority is to get the water down the river to Menindee and the Darling," she said.

Cotton industry 'comfortable' with water use

Meantime, Chairman of Cotton Australia and south west Queensland irrigator Hamish McIntyre said that where the reach commitments had been met from an environmental perspective, there had been some water harvesting announced in Queensland.

"Queensland has completed all their water resources plans and they've been accredited by the Murray-Darling Basin Authority.

"Resource operating plans in all reaches of the river are there [and] set, so all we can do as irrigators in each reach of the system right throughout is meet those commitments.

"[Wilcannia] is a long way down there … and flows from way back up in Queensland starting around Warwick and Toowoomba, historically have struggled to get there."

Mr Mcintyre said he was very comfortable with irrigators starting to take their water entitlements in Queensland as long as it had met the requirements from an environmental point of view.

"We feel very strongly for those people, but we do need to still operate under existing plans [that are] in place and the embargoes are helping meet those commitments.

"I hope what's been put in place will actually do the job for those people at Wilcannia, from a New South Wales perspective, but Queensland historically, from where the water is flowing at the moment, will struggle to help in that area," Mr McIntyre said.