The Department of Primary Industries has sent staff to examine the Menindee Weir Pool region, south-east of Broken Hill, where banks are lined with dead bony bream, Murray cod and other species following a “shocking” algal bloom event.

Community members and farmers blamed the Murray-Darling Basin Authority, acting at the behest of the state government, for draining the Menindee Lakes twice in four years, leaving fish stuck in stagnant pools.

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MDBA chief executive Phillip Glyde responded to the accusations on Thursday, saying the “tragic” fish deaths in the Lower Darling are “a terrible reminder of the effects drought can have on our environment”.

“Unfortunately, the main causes of this distressing event are the lack of water flowing into the northern rivers, and the impact of 100 years of over-allocation of precious water resources throughout the entire basin,” he said in a statement.

“Lack of water during drought leads to water quality issues, and can provide prime conditions for blue green algae to thrive. When previously high water temperatures drop quickly, as they did briefly recently, algae dies and as it decomposes oxygen levels fall below critical levels, causing the fish to die. Without more water available to flow through the system, it is possible more fish will die during summer.”

With rivers running dry and water storages across the northern Murray–Darling Basin at 20 per cent, drought conditions are affecting communities, businesses, animals and the environment.

“This is upsetting and a concern for local communities, businesses and authorities,” Mr Glyde said.

“It is understandable that people are looking for answers. Some have alleged that the operation of the Menindee Lakes has caused water quality problems and the fish deaths.

“The Menindee Lakes are currently under the sole control of New South Wales. This occurs when the water in storage falls below 480 gigalitres as it did in December 2017.

“There is a written agreement where New South Wales, Victoria, South Australia and the Commonwealth direct the Murray–Darling Basin Authority (MDBA) to call water from the Menindee Lakes to meet consumptive and environmental needs. This agreement dates back to the 1960s when the lakes were developed as a storage. The agreement reflects the fact that when the Menindee storages were created they impeded flows of water through to Victoria and South Australia.”

Mr Glyde said the MDBA draws water from the Menindee Lakes first because Dartmouth and Hume dams don't have the high evaporation rates of the Menindee Lakes.

“The figures speak for themselves, Menindee Lakes can hold up to 2,050 gigalitres and is estimated on average to lose 426 gigalitres a year to evaporation, and up to 700 gigalitres a year when the lakes are full. Dartmouth Dam, by comparison can hold up 3850 gigalitres with evaporation of close to zero,” he said.

“When it comes to drought none of us can control the weather. But we can control the level of use and that is where the Basin Plan comes in.

“With bipartisan agreement, from six jurisdictions, governments agreed to the Murray–Darling Basin Plan in 2012. The Basin Plan won’t be fully implemented until 2024 so we’re halfway through and it will take decades to reverse the effects of 100 years of over allocation of water but we’re on the path.”

The cotton industry has also come under fire as a result of the incident, with environmental groups claiming irrigators are “choking the life” out of the river system.

Jeremy Buckingham, the former NSW Greens and now independent MP, said the Darling River "is dying right before our eyes".

“The huge extraction of water for big irrigators is literally choking the life out of the system downriver and leaving stagnant, blue-green algae infested dregs for everyone else," he said, arguing that the Menindee Lakes had been drained "to spare upstream irrigators from contributing more water for the environment".

Cotton Australia has issued its own statement in response to the claims, saying while the fish deaths were a “devastating sight”, it is wrong to blame cotton growers for the incident.

“About 18 months ago, 2,000 gigalitres of water was in the Menindee Lakes before the Murray-Darling Basin Authority took the deliberate decision to accelerate releases from Menindee to meet downstream requirements and reduce overall evaporation losses from the Lakes,” Cotton Australia general manager Michael Murray said.

“In hindsight, this was probably a poor decision, but it does highlight the incredibly difficult task of managing flows in a manner that minimise losses, but ensures enough water is available for communities and the environment during extended severe droughts.

“Since July 1, 2017, irrigators have extracted just 16 gigalitres out of the Barwon-Darling – an amount that would have evaporated out of Menindee in just 16 days.

“Coupled with the extensive drought and the simple fact there has been little-to-no rain, the release of water from the lakes has exacerbated the conditions leading to these fish deaths.

“What this issue highlights is how difficult the management of the Menindee Lakes is. We welcome the investigation into the fish deaths by the NSW Department of Primary Industries and WaterNSW.”

Mr Murray said the drought is impacting all agricultural sectors, including the cotton industry which is expected to produce only half the volume of last season’s crop this year.

“On the Barwon-Darling, the impact on cotton production is even more devastating with zero hectares of cotton being grown in Bourke this season, down from 4,000 hectares the year before,” he said.

“Further upstream at Dirranbandi (home of Cubbie Cotton), just 300 hectares of cotton has been planted, which is one per cent of what can be planted in a very good season.

“Cotton Australia is very proud of our industry that produces a quality fibre that is in demand both here at home and around the world; but as an industry we are growing very tired of being ‘the whipping boy’ for all the problems that are being brought on by this crippling drought.”