A man has died after being swept into a stormwater drain in Sydney during flooding that has caused chaos and prompted rescues.

The man was working at a waste management and recycling centre at Lucas Heights when he was overcome by the surging rain water.

Police Superintendent Julian Griffiths says neither his workmates or emergency services were able to save him.

"The worker appears to have called for assistance and his fellow workers have tried to come to his aid," he said.

"Unfortunately from the site as it appears and from the information that we've got the heavy rain caused that area that they were working in to fill quite quickly with water."

His body was retrieved by police officers a couple of hours later.

Two people have also been taken to hospital after being struck by lightning during the storm.

Several people were rescued from their cars by the New South Wales State Emergency Service (SES) during the downpour.

There was flash flooding at Mascot, Bankstown and Zetland.

The SES has responded to more than 300 calls for help, mostly to manage fallen trees and damage to houses.

The Parramatta River overflows during the downpour. ( Jessica Kidd, ABC News )

The heavy rain has led to an oil spill from the Caltex oil refinery into Botany Bay at Kurnell.

Caltex says it is working with the Sydney Ports Corporation to contain and disperse what it describes as a small oil release.

The company says all relevant authorities have been notified about the spill.

Downpours of over 70 mm of rain in less than an hour have been recorded at Cronulla, while 55mm of rain fell at Cronulla South Bowling Club and 64mm in one hour at Audley at 2.53pm (AEDT).

Phil Campbell from the SES says drivers have been rescued from six cars caught in the flash flooding.

"We have now had six flood rescues the SES has been called to this afternoon, most of those have been in south west Sydney and also around the inner city particularly in the Waterloo, Zetland area," he said.

"These have been for people who have driven their cars into localised flash flooding."

Mr Campbell says conditions in Sydney's north have eased but the south-west, Illawarra and Sutherland Shire are now bearing the brunt.

"We are expecting further very heavy rain with thunderstorms this evening and localised flash flooding," he said.

Sydney's public transport network is affected, and travellers are being asked to allow extra time.

Transport NSW says the South Coast rail line is partially closed between Waterfall and Thirroul.

Buses are replacing ferries between Rydalmere and Parramatta on the Parramatta River because the Parramatta Weir is overflowing.

Audley Weir in the Royal National Park is closed in both directions because of flooding.

Wolli Creek in Sydney's south is flooded.

Drivers are being advised to slow down and avoid flooded areas as heavy rain continues to pour.

The SES says the wet weather will continue for the next 48 hours.