Thousands of people in Greater Sydney have been ordered to flee their homes as the flood crisis gripping NSW continues, with severe weather and heavy rain battering vast swathes of the state.

Emergency Services Minister Steph Cooke says Greater Sydney, and the Central Coast are facing 'treacherous' weather conditions, with the next 24 hours critical.

Major flooding is expected along the Hawkesbury and Nepean and Georges rivers, at Menangle, North Richmond, Penrith and Windsor on Thursday.

The State Emergency Service received 3166 calls for help in 24 hours and overnight issued more than 60 evacuation orders and 20 evacuation warnings.

Tens of thousands of people living in Sydney's west, northwest and southwestern suburbs including Windsor, North Richmond, Camden and Milperra, were ordered to flee to safety.

The Bureau of Meteorology is warning of life-threatening flash flooding and damaging winds with peak gusts in excess of 90 km/h.

SES assistant Commissioner Sean Keans says a looming east coast low off Newcastle will bring heavy rain to the Hunter, the Central Coast and Sydney, the Illawarra and the South Coast from Thursday morning.

"That's going to bring with it up to 250mm of rain over a two to three hour period which can be really dangerous and it's also going to bring strong wind, so we are asking people if they can avoid unnecessary travel," he told Sydney radio 2GB.

River levels are rising extremely fast due to the sheer volume of rain, with flood levels along the Hawkesbury-Nepean set to be worse than those which affected the area in March 2021.

"The flooding is going to be higher this time," Mr Keans warned.

The Nepean River at Penrith will reach nine metres bringing moderate flooding, the Hawkesbury River at North Richmond will reach 15 metres bringing major flooding.

At Windsor, the Hawkesbury River will reach 14 metres by Thursday night - two metres above its major flood level.

Residents in western Sydney who endured floods in the Hawkesbury-Nepean region in March last year were told to leave on Wednesday evening after around 600 gigalitres of water flowed over the Warragamba Dam wall.

Ms Cooke said that would have a significant impact downstream with about 130,000 homes in the path of the overflowing dam.

She urged people to heed evacuation orders but avoid leaving home unless told to by the SES - and to be aware of other risks such as falling trees .

NSW Health said people isolating due to COVID-19 who need to evacuate their homes must leave.

"If you are told to evacuate, you must evacuate," acting Chief Health Officer Marianne Gale said.

"Under no circumstances should you remain in self-isolation at your residence - your safety is our highest concern and an emergency evacuation is a valid reason to leave your home."

NSW Health advises COVID-19 positive people at flood evacuation centres to notify staff, wear a mask and physically distance from others.

In Lismore on the north coast the clean-up continues as the death toll rises, with four fatalities confirmed in the region's flood event so far.

The devastated town is also facing food shortages with supermarket shelves empty and petrol shortages. Residents are reporting ATMs have run out of cash.

Two women in their 80s and a man in his 70s were found dead in their flooded homes, while another man's body was found floating down a Lismore street.

A fifth man died on the Central Coast last Friday morning after his car was swept away in floodwaters.

© AAP 2022