Continuing heavy rain has forced the evacuation of more than 320 properties in St Georges Basin and Sussex Inlet on the New South Wales south coast.

Meanwhile, the Bureau of Meteorology (BoM) warned the Warragamba Dam was expected to spill overnight and could cause minor flooding of the Hawkesbury and Nepean Rivers, west of Sydney.

Key points: 320 properties evacuated in St Georges Basin and Sussex Inlet

320 properties evacuated in St Georges Basin and Sussex Inlet Flood peak expected later tonight

Flood peak expected later tonight Warragamba Dam expected to spill; minor flooding of Nepean and Hawkesbury rivers expected

The State Emergency Service (SES) said there had been more than 1,600 calls for help and 79 flood rescues since the severe weather began earlier this week.

Homes and buildings have been damaged, schools closed and there were fears the Jerrara Dam would fail, west of Kiama.

The all-clear has since been issued for properties downstream of that dam.

The weather bureau's acting regional director, Stephen Lellyett, said in a statement the Warragamba Dam was expected to spill for the first time in two years.

Mr Lellyett said up to 160 millimetres of rain had fallen in the Wollondilly River upstream of the Warragamba Dam in the 48 hours to 9:00am on Wednesday.

"At this stage, with Warragamba Dam expected to spill overnight, minor flooding is likely along the Hawkesbury and Nepean rivers, similar to flooding seen in March 2012," he said on Wednesday.

Sorry, this video has expired Heavy rain floods parts of Sussex Inlet

Earlier on Wednesday at Saint George's Basin, the SES said flood waters were expected to inundate up to 80 properties but authorities are yet to finalise the number of homes affected.

Up to 320 properties in St Georges Basin, Sussex Inlet and Sanctuary Point on the south coast have been evacuated.

SES team leader Anthony Jarvis said the flooding was some of the worst he had experienced.

"Being my first major one, it's bit scary out there. It's hard to comprehend until you're really out there and in the thick of things," he said.

More than 400 millimetres of rain has fallen since Tuesday at Sussex Inlet and some streets are a metre deep in water.

The flood waters were expected to peak at Sussex Inlet overnight.

Car flooded at Old Erowal Bay at St Georges Basin. ( ABC News: John Gunn )

Deputy Commissioner Newton said most residents remained calm in the face of evacuation requests.

"We've had a mixed response. A large number of people evacuated when we put the initial warning out last night," he said.

"We have, through the day, been in communication with other residents who decided to stay and look after their properties and a number of them have subsequently evacuated in the course of the morning as the water's risen around them."

'It's completely engulfed our house'

SES spokesman Phil Campbell said people have had to take refuge at the bowling club in Sussex Inlet or at the country club in Sanctuary Point.

"We are pleased to see that the number of flood rescues has been declining," he said.

Rose Sinclair and her daughter were rescued from their Sussex Inlet home by boat.

"We were nervous... We didn't expect anything like this. But we'll be alright," she said from the local evacuation centre.

"[We were] a bit scared at first but we've calmed down a lot, but we don't know if we'll be here all night. We hope not."

Flooding at St Georges Basin. ( ABC News: John Gunn )

Mia Hill and her two children were rescued by the SES after their Sanctuary Point home was threatened by the flood waters.

Ms Hill said she made the call early to get out.

"It's completely engulfed our house. We're high-rise, but we're flooded in," she said.

"The weather was meant to stay here all night and I just didn't want to take the risk. The deeper it gets the more dangerous it gets, so we had to get out."

Flooded roads at Sussex Inlet. ( ABC News: John Gunn )

Residents of Shoalhaven Heads said flooding in the area could have been prevented if the local council acted more quickly to mechanically open the Shoalhaven River opening to the ocean.

Forty residents have been evacuated from the town because of rising flood waters.

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Resident Phil Guy said his home on Hay Avenue was already inundated.

"They would have had more than ample time yesterday but obviously it's too late now," he said on Wednesday.

The Shoalhaven City Council said the Shoalhaven River mouth had been opened by contractors.

Meanwhile, an electrical sub-station exploded on Hyams Street at Nowra on the south coast and authorities believed the blaze was sparked due to heavy rainfall and flooding in the area.

Schools affected, BoM issues flood warning

Roads are impassable and many residents have had to leave their homes as floods affect Sussex Inlet and St Georges Basin. ( ABC News: John Gunn )

Kiama had its wettest day in 13 years with rainfall of 230 millimetres.

The Department of Education said Bulli High School was open for classes for senior years, with supervision provided for years seven to 10.

Terara School was closed, with supervision provided at Nowra East Public School.

St George's Basin, Berry and Sussex Inlet schools were open.

Parts of Lake Conjola were inundated by flood waters with some areas of the small township already isolated.

The SES said the main bridge in the town was also covered by flood waters due to the rising lake levels and had been closed.

Flood warnings were also issued for Nowra and Terara as well as the Belubula River at Canowindra and the Snowy River in Victoria.

Floodwaters may cause sewage contamination

People near rising floodwaters are being warned to stay away from polluted water, or risk infection.

Director of Shoalhaven Water Carmel Krogh said flushing may not be clearing toilets at locations such as Sussex Inlet, Conjola and St George's Basin.

She said it was important not to enter floodwaters that could be contaminated.

"Particularly in areas that have floodwaters around them, it's very, very important for people not to be wading through those waters or playing in them or entering them, not just for safety but because they could be contaminated with sewage," she said.