However bureau meteorologist Jake Phillips said relief from the rain was not far away.
"It does look like some areas could still see some pretty decent rain persisting into tomorrow as well, although it will start to become a lot more localised," he said.
"The system that’s generating all this weather will start to lose impact from later today, but then more so as we progress through Friday.
"So for Saturday for that area … it still does look like there could be a couple of showers hanging around but nothing of great significance."
In Sydney, Thursday's weather will be "bleak" but will clear by the weekend.
"We’ll see quite a few showers passing through at times but we're not expecting anything particularly heavy around Sydney," Mr Phillips said.
"Some spots might receive five, maybe 10mm of rainfall at the most today in Sydney."
The heaviest rainfall for Thursday is forecast for the Mid North Coast and Northern Tablelands, and already some towns are experiencing flooding.
In Dungog, Hooke Street flooded, after the town received more than 287mm of rain in 48 hours.
Other places likely to be affected by rain include Coffs Harbour, Port Macquarie, Taree, Kempsey, Sawtell, Dorrigo, Nelson Bay and Yarrowitch.
Careys Peak, near Barrington Tops, received 186 mm of rain to 9am on Thursday and Tuncurry recorded 194mm in the same period. Williamtown, in Port Stephens, recorded 122mm and Maitland recorded 120mm.
SES Deputy Commissioner Greg Newton told Nine News the high rainfall meant flash flooding was still a "real risk" for areas from Newcastle up to Taree.
A flood watch warning is still current for parts of the Central Coast and the Mid North Coast on the weather bureau website.
Rachel Clun is a reporter at the Sydney Morning Herald. She was previously a reporter with the Brisbane Times and Domain.
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