The head of the Murray-Darling Basin Authority has warned of dire conditions across the crucial river system, with the situation expected to worsen during a hot and dry summer.
MDBA chief executive Phillip Glyde said the most critical situation was in the drought-ravaged northern basin, where some water storages were as low as "one or two per cent".
“Conditions are dire in the north,” he told a Senate estimates hearing in Canberra on Friday.
Total storage in the basin is at 39.7 per cent with the southern basin at 44 per cent.
“While not as dire, if there is no significant rainfall in winter and spring next year, the southern basin's water resources will also be severely limited,” Mr Glyde said.
The Bureau of Meteorology found the 33 months between January 2017 and September this year were the driest average on record across the basin.
The bureau has also forecast low flows for the rest of spring and summer, with a warm and dry pattern likely to continue through to January.
“These conditions continue to place immense pressure on communities, industries and the environment,” Mr Glyde said.
“Sadly the basin cannot be drought-proofed. Drought is a natural part of Australia's climate.”
Low rainfall across the basin is also having an impact on water quality, with Mr Glyde warning of tragic consequences for native flora and fauna.
“We are expecting more fish deaths, and water quality issues like blue-green algae this summer."
He said "high security" water entitlement holders could expect allocations, but those in lesser categories were likely to remain without unless it rained.
“It is important to note that all water entitlement holders are treated the same, regardless of whether water is for farming or for the environment.”
Mr Glyde acknowledged that made it hard for farmers without allocations to see water flowing in the river when their crops were suffering.
He said the water was there because entitlement holders carried their allocation over or stored water from previous years in a business decision not to access it.
Commonwealth Environmental Water Holder Jody Swirepik told the committee the watering her organisation had undertaken was based on methodical planning and the best science.
“Current environmental water use is having no impact on water allocation for drought-affected farmers,” she said.
Nationals senator and committee chair Susan McDonald said the Murray-Darling Basin was probably Australia's most important issue.