Intense flooding followed by warm, sunny weather along the NSW coast is causing fish deaths and bad smells, the state's Environment Protection Authority says.
EPA director regulatory operations Adam Gilligan said "blackwater" events were caused by low oxygen levels in the waterways.
Floodwaters would have picked up organic matter, like decaying vegetation and leaves, from low-lying areas surrounding rivers.
Mr Gilligan said the decomposition of this matter was an "important process for health river function" but depleted oxygen levels in the water, releasing tannins which turn the water black.
"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," Mr Gilligan said in a statement on Friday.
"Blackwater after flooding is a natural feature of Australian river systems and the capacity to prevent and manage the impacts of blackwater is limited."
The EPA detected dead fish and odours while out sampling last Tuesday in the Hunter River from Raymond Terrace to Sandgate. Low oxygen levels were identified.
The agency says it will support local councils by sampling floodwaters and offering advice.
It warns there is a heightened risk that river water will contain infectious organisms and chemicals.