The state's department of primary industries and fisheries has received reports of fish deaths in Hunter River, Wallis Lake and Macleay River.

It is not unusual for large numbers of fish to die following floods and it can affect water quality and impact native fish populations, the department said.

Odours from receding floodwaters are likely to be caused by natural processes due to low levels of oxygen in the water, Environment Protection Authority director of regulatory operations Adam Gilligan says.

"The recent significant rain elevated water levels in many rivers. As the floodwaters moved over low-lying areas surrounding the rivers, they picked up large quantities of organic matter, including decaying vegetation and leaves, as well as dirt, sand and other debris," he said.

"Although an important process for healthy river function, the decomposition of organic matter depletes oxygen levels in the water and releases tannins which give the water a distinctive black colour.

"This natural process is commonly known as 'blackwater' and is likely to cause fish deaths in rivers.

"The stagnant water also contributes to the odours which can smell like rotten egg gas."

Not much could be done to prevent the process, he said.

The EPA has been testing water quality at various flooded sites and warns residents not to swallow any river water.

Australian Associated Press