The severe drought, stagnant water and devastating bushfire have combined to cause the death of thousands of fish in the Macleay River since late November last year.
Recent rainfall across the region has washed organic matter, sediment and ash from the Carrai East fire into the Macleay River.
The pollution has resulted in decreased water quality and a rapid drop in oxygen levels to the river, which had previously become stagnant in the upper regions of the Macleay.
NSW Department of Primary Industries (DPI) are investigating the reports of fish deaths in the upper and middle reaches of the Macleay River.
"Current rainfall events across the region are adding ash from the extensive bushfires throughout the region into local catchments, as well as other organic matter and sediment," a NSW Department of Primary Industries spokesperson said.
"In some cases this is accumulating in the refuge pools in which fish have gathered as the available water in the river has reduced because of the ongoing drought.
"Fish can be directly impacted during fires through excessive temperatures or loss of habitat, or be threatened from rapid declines in water quality if rainfall occurs in recently burnt areas."
DPI predict fish deaths in the river will continue as more rainfall is forecast to fall in fire affected regions.
"Fish kills may continue to be reported this week with rain predicted to fall across fire affected catchments," the spokesperson said.
Concerned Upper Macleay resident Arthur Bain discovered hundreds of dead fish near the Bellbrook bridge last Saturday January 11.
The heavy rainfall at Armidale resulted in an increase flow of ash into the Macleay River, which reduced the oxygen in the water and caused the mass fish kill.
Mr Bain claims there were reports of hundreds of more dead fish further up and down the river.
"This is what happens when there are unprecedented bush fires," Mr Bain told the Argus.
"Even the local Indigenous elders I have spoken to said they have never seen or head of anything like it. It's what happens when we don't take care of the environment."
DPI Fisheries is working with local landholders to continue to monitor the situation.
The NSW Government's $10 million commitment to support native fish during the current drought and bushfire season will be critical in assisting the recovery of populations when conditions improve.