The Menindee Lakes are expected to start filling up again soon as water from floods in northern New South Wales earlier this year reaches the area.
Barry Philp from State Water in Menindee says the Darling River has started flowing again at Wilcannia, and this water will reach the lakes within a few weeks.
He says the smaller of the Menindee Lakes will be filled first.
"First off we'll place that water in Lake Wetherell and bring Lake Wetherell back up to full supply and then potentially place further water in Lake Pamamaroo," he said.
The faster flowing water is expected to flush out the blue-green algae that has plagued the Darling River at Wilcannia.
A bloom broke out just north of the town earlier this year in stagnant, warm water.
Mr Philp says floodwater from the Macintyre, Dumaresq and Severn river has now passed through the Darling River at Bourke.
"Those floodwaters are just starting to flow into Wilcannia at the moment," he said.
"All floodwater carries a bit of turbidity in it - which is good quality water - so that should break down the algae in that stretch of the river."
None of the floodwater from this weekend's storms in north-eastern NSW is expected to reach the Darling River.
"Anything this side of the Great Dividing Range will flow into this system but all those flows in Macleay and Hastings and the Mann River, all those rivers are on the north-east side of the Great Dividing Range so, no, they won't flow into this section of the river," Mr Philp said.
Mr Philp says the slightly cooler, cloudy weather this week has halved evaporation in the Menindee Lakes to about eight millimetres per day compared to the start of January.
© ABC 2013
13:45 EST The vast majority of Queensland has endured one of its warmest and driest autumns on record, but the southeast was soaked.