The Department of Primary Industries says oxygen levels in the Hunter River are starting to increase after a mass fish kill earlier in the week.
Thousands of dead fish have been found in the river as floodwaters flow downstream.
Both the DPI and Environment Protection Authority have conducted water testing and say low oxygen levels brought on by the recent flooding is to blame for the kill.
They say large amounts of decomposing vegetation is consuming the oxygen that the fish rely on.
The DPI's Sarah Fairfall says she expects fish stocks to recover quickly.
"We've done research on the Richmond River, where we had a very similar type of kill occur there in 2008 and also in 2001 following some flooding," she said.
"In 2008 we had scientists on the river a month later and they couldn't indicate any significant difference with the fish stocks," she said.
"So it's amazing how quick the river can come back."
© ABC 2013
19:53 EDT Wind gusts of up to 90 kilometres an hour brought down power lines, cut traffic lights and delayed public transport across Sydney this afternoon.