A renowned angler says a mass fish kill in the parched Macquarie River in New South Wales this week left the waterway looking like "tomato soup."

Key points: Thousands of fish died in the Macquarie River at Dubbo this week after rain caused a sudden shift in the water's oxygen level

Thousands of fish died in the Macquarie River at Dubbo this week after rain caused a sudden shift in the water's oxygen level Ecologists say more fish kills are likely with each new rainfall event, and that some species are at risk of dying out locally

Ecologists say more fish kills are likely with each new rainfall event, and that some species are at risk of dying out locally Dissolved oxygen levels in the river remain at critically low levels, and the NSW DPI is working on fish "insurance populations"

Tens of thousands of fish of all sizes and species are estimated to have perished near Dubbo, in the state's west, after much-needed rain washed sediment into the river, causing dissolved oxygen levels to drop rapidly.

Fisher Matt Hansen said he was staggered by the result.

"It looks like someone's tipped out a ute-load of mulch on the edge of the bank," he said.

"It's actually dead shrimp.

"I've never seen the water like this — it's alarming to see.

"The river looks like tomato soup."

While rain is the only thing that will break the drought, ecologists are warning fish deaths could occur in the Macquarie River with each new rain event, and could render multiple species locally extinct.

The risks of run-off

Professor Lee Baumgartner, a river management expert from Charles Sturt University, said silt can be deadly for fish during droughts.

"Run off from rainfall can quickly lead to deteriorating water quality and this, in turn, can have adverse impacts on aquatic biota," Dr Baumgartner said.

Thousands of fish were killed in the Macquarie River in western NSW last week. ( Inland Waterways OzFish )

He said excess inflows of silt and nutrients created a spike in bacteria.

As the bacteria respired, it took huge amounts of oxygen out of the water, suffocating the organisms in it.

Dr Baumgartner said silt could also destroy habitats and clog fish gills, and that the risks of more fish mortality events would not abate until the Macquarie River was fully flowing again.

"If there's not enough flow along the river to carry the dumped silt then it will simply accumulate in the pools where it's dumped and have a huge localised impact," he said.

Dr Baumgartner said the risk of fish deaths after rain events were much higher in areas impacted by drought and bushfires.

"In the Upper Lachlan in the 1920s there was a period of drought, then a bushfire, then a rain event which washed nutrient, ash and charcoal into the river," he said.

"Fishermen in the area said they never caught a Murray cod again after that."

Hundreds of native fish have been caught from the Macquarie River and relocated to hatcheries to create an "insurance population". ( NSW Department of Primary Industries Fisheries )

Extinction crisis looms

After three years of record-low rain fall, the Macquarie Valley is one of the worst drought-affected regions in the country.

It is possible the Macquarie River, which is currently running, will start to dry out by October.

After that, fish stock and wildlife may be constrained to deep pools.

The southern purple-spotted gudgeon and the olive perchlet, two rare species that have not been seen for some time in the region, are at immediate risk of extinction, according to the NSW Department of Primary Industries (DPI).

DPI senior fisheries manager Sam Davis said efforts have been made to rescue the last-known populations of these two species from the Macquarie and relocate them to hatcheries until conditions improve.

"Our fish rescue strategy is not just about the big iconic fish that people love to catch and eat," Ms Davis said.

"It's also about the small-bodied fish that fly under the radar which are equally vulnerable."

Other species at risk of extinction include the Oxleyan pygmy perch, Macquarie perch, silver perch and eel-tailed catfish.

Ms Davis described the threat of more mass deaths as "extremely concerning".

"Since European settlement our native fish stocks are estimated to have declined by 90 per cent," she said.

"So we're already starting from low numbers."

The Macquarie River is dammed at Burrendong near Wellington. The storage is now below two per cent capacity. ( Mick Williams - Inland Waterways OzFish )

Creating an insurance population

This week's fish kill follows other bushfire-related mass deaths on the NSW South Coast and in the Macleay River on the Mid-North Coast.

Poor water quality events are also emerging in the Snowy Mountains and north-east Victoria.

For the past year the NSW DPI has deployed strategies ranging from rescuing and relocating fish to implementing technology to improve water quality.

Last year, more than 220 native fish were saved by hand and are now being used in hatcheries to breed an "insurance population".

As water levels drop, several aerators have recently been installed to boost oxygen levels in key fish refuges and keep isolated populations alive until the drought breaks.

"We have known areas that are going to be impacted by low oxygen levels and algal blooms," Ms Davis said.

"We need to intervene there first and foremost."

Artificial aeration devices have been installed to keep native fish species alive in drought-stricken inland rivers. ( NSW Department of Primary Industries Fisheries )

Can we stop the Macquarie drying up completely?

With little rain on the horizon, Water NSW, the state's bulk water supplier, is running out of options to transfer water down the Macquarie River.

In February, 25 gigalitres will be transferred to the Macquarie Valley's main dam, the Burrendong Dam, from Windamere Dam near Mudgee.

This water would be sent downstream to communities in western NSW for critical needs water.

After three years of record-low inflows, Burrendong Dam is now below two per cent capacity.

New pumps are being installed to provide access the deep, silty water sitting on the dam's floor.

This water would be sent downstream from May to October.

A Water NSW spokesperson said in a worst-case scenario, the Macquarie River would cease to flow by October.

Flows have already ceased downstream of the township of Warren, 115km north-west of Dubbo.