The agency responsible for commonwealth-held water entitlements has strongly criticised New South Wales and its management of the Barwon-Darling river system.

The Commonwealth Environmental Water Holder says current NSW operating rules benefit cotton irrigation over other river users – including uses that should be given higher priority in the state’s water legislation.

The comments, contained in a submission to the NSW Natural Resources Commission, underscore the tensions in managing the upper part of the Murray-Darling system, particularly since the major expansion of irrigation between Mundindi and Bourke over the last two decades.

The early review of the Barwon-Darling water-sharing rules – one of the most contentious elements of the basin plan – was prompted by the three fish kills at Menindee Lakes, allegations of water theft which are now before the courts, and concerns about how the plan was drawn up.

Jody Swirepik, the commonwealth environmental water holder, blames the Barwon-Darling rules for prolonging drying events in the Upper Darling, leading to serious environmental and social ramifications.

Unlike other parts of the river system, this part of the river is ephemeral, meaning its flows can vary greatly from mighty flows to just a trickle. The Barwon-Darling is also “unregulated” as it has few dams to store water.

The rules about when irrigators can pump are usually tied to the height of the river measured at various points.

“According to work by Associate Professor Fran Sheldon, cease-to-flow conditions have occurred more often and for longer in recent decades,” Swirepik argues. “This has profound environmental and social consequences.

“From a social perspective, low flows are important for improved water quality for town water supplies, algal bloom risk mitigation, reduced frequency of salinity spikes, and social wellbeing of communities, including Aboriginal communities.”

She suggests that instead the rules have led to economic uses being given priority.

“The CEWH appreciates that water-sharing during droughts is particularly challenging and contentious. It is important that equitable water-sharing arrangements are founded on a clear articulation of priorities for access to water, particularly when there is insufficient water to satisfy all demands for water.”

The CEWH is particularly critical of the way the rules operate to allow water to be extracted for economic purposes – primarily growing cotton – at the expense of users who are ranked higher priority under legislation, such as townships along the river, graziers who need water for stock and Indigenous communities.

CEWH singles out rules that allow irrigators to take 300% of their allocation in one year. This means that irrigators can have unused allocations in their water accounts and, when it begins to rain, they can extract huge volumes.

“The taking of such large volumes of water under these circumstances can significantly prolong dry periods in the lower parts of the Barwon-Darling river system,” she says.

Although the NSW minister can impose an embargo on irrigation or irrigators can collectively choose to not pump the resumption flow after a cease-to-flow event, Swirepik says these are inadequate protections.

Instead she is calling for rules that do not require a specific orders from the minister and automatically protect these first flushes of the river system after rain.

The plan also has rules that discriminate against the environmental water holdings, she says.

The CEWH has bought several properties along the river but the moment the commonwealth buys the property for environmental purposes, it loses the rights to carry over water and manage the water as the irrigator had. Instead it must use 100% of the entitlement each year.

Cotton Australia on the other hand is highly critical that the review of the Barwon- Darling water-sharing plan has been brought forward, saying it had been inappropriately triggered by the fish deaths.

“Cotton Australia would have more confidence in the motivation for this review if it hadn’t been spurred on by the fish deaths, which appear to have been caused by multiple and inter-related factors, only some of which will be considered in this review,” the peak body says.

“It appears to Cotton Australia that the Barwon-Darling water-sharing plan area has become somewhat of a ‘lighting rod’. It also appears to bear an undue level of both criticism and scrutiny.”

Cotton Australia says the plan preserves 94% of annual flows for the environment but this claim was directly criticised by the CEWH.

“This figure is used to imply that 94% of the water in the Barwon-Darling river system in any given year flows directly to support the environment,” Swirepik said.

“The problem with the long-term average statistic in the Barwon-Darling is that it is dominated by a few large floods (including two in the 1950s). Floods make up the majority of the total volume in the hydrological modelled record and dominate this average statistic and the impression it gives.

“An average such as this ignores critical events, including low-flow events and cease-to-flow events, and, by itself, is misleading.”

The Australian Floodplains Association, which represents many of the graziers downstream from Bourke, and the Wilcannia Aboriginal community, says there is much to be learned from the 50,000 year experience of the original inhabitants along the Barwon-Darling.

“These long-standing inhabitants and communities with a strong cultural, social and economic attachment to the Darling are convinced that over-extraction for irrigation in the upper reaches of the Darling system will destroy both the river and their communities unless the over-extraction is addressed,” it says in its submission.

The commission is expected to release its report next month.