Flooding followed by warm, sunny weather has sent a stink over parts of Port Stephens, particularly in Raymond Terrace.
The severe floods across large parts of NSW last month are causing fish to die and unpleasant odours are emanating from some waterways.
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 said.
"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."
The EPA was out sampling water from the Hunter River between Raymond Terrace to Sandgate on March 30 and has identified low oxygen levels.
Mr Gilligan said the EPA is supporting councils and other government agencies by sampling flood waters and providing advice.
"The EPA will continue taking samples and testing water sites where required. We encourage the community to be patient and to make contact with the EPA if they have concerns about polluted waterways in their area,"
Entering river water after heavy rain increases the risk of injury and infection. If you have swallowed river water and become ill, seek medical advice.