Environmental agencies are warning there could be widespread blackwater events, fish kills and blue-green algae outbreaks across the Murray-Darling Basin due to the huge amounts of water in the river system.
Rivers across inland New South Wales and northern Victoria have been in flood for weeks, pushing large volumes of water across vast flood plains.
Murray Darling Basin Authority (MDBA) environmental management senior director Janet Pritchard said while the water would bring long-term positive impacts to the basin's flora and fauna, in the short term there would likely be impacts on water quality.
"There's such huge volumes of water involved, our options to do anything about it are very, very limited," she said.
The New South Wales Department of Planning and Environment (DPIE) says its main concern over coming days is the emergence of hypoxic black water events.
"That's when you get a lot of organic material entering the river as it flows in from the flood plain," DPIE water implementation manager Allan Raine said.
"The critters that feed on that organic material use oxygen and, as temperatures go up, they become more active and you can end up in a situation where there's so much oxygen utilised in the water column, it becomes difficult for fish to survive."
Mr Raine said low oxygen levels have already been recorded in the mid-Murray River around Echuca-Moama, in the lower Murrumbidgee River at Balranald and in the Barwon River between Walgett and Bourke.
The MDBA said there had also been reports around Echuca-Moama of Murray crayfish leaving the water, and stressed fish being seen on the river's surface.
"The Commonwealth Environmental Water Holder is using some of Murray Irrigation's channels and they're providing small amounts of better-quality water in through those escapes [to the river] and that's just helping provide small places for the native fish to retreat to," Dr Pritchard said.
She said the additional flush of water would not exacerbate flooding in the river.
'A perfect storm'
The DPIE said as summer approaches there was also the potential for fish kills and the emergence of blue-green algae.
"As air temperatures go up, water temperatures go up so we're keeping a very close eye on that because we may see fish deaths occur if the temperature continues to rise," Mr Raine said.
"There's a little bit of a perfect storm happening in that we're currently on high alert for blue-green algae in the Hume Dam, but again when the weather warms up we're keeping a close eye on that too."
Dr Pritchard says it is unclear how widespread water quality impacts will be, and if there will be an effect on the South Australian Murray as the floodwaters move south-west.
'It's just a little bit too early tell; we're just on the cusp of the hotter summer months and we're not sure how bad it could get," she said.
