Hamilton, Kotara and Merewether all experienced rising water, which disrupted traffic flow and damaged cars.

Westfield Kotara shopping centre was hardest hit with more than 30 cars inundated by water in the car park and part of the ceiling of Michael Hill Jewellers on the first floor falling in.

Newcastle Permanent was damaged with one panel of its automatic door shattering.

Shoppers who had used disabled parking spaces returned to their cars to find them flooded and unable to be driven.

Barbara Lancaster had travelled from Fern Bay Village and returned from shopping to find her Hyundai Sonata completely soaked.

"I came out to see the water half way up the doors," she said. "I'm waiting for my son-in-law to pick me up and go to the NRMA."

Many customers spoke of a lack of communication, being told to stay inside while the car park flooded and then told, shortly afterwards, to evacuate the centre.

Westfield Corporate Affairs manager Julia Clarke said a number of shops closed between noon and 1.30pm mainly due to safety concerns but a small number will remain closed.

"Just why those retailers still closed have been affected by the heavy rains to such an extent is still being investigated," she said.

Nobbys recorded 28.4 millimetres of rain in half an hour, beginning at 12.16pm, and 32.8 millimetres by 3pm.

State Emergency Service Hunter Region controller Greg Perry said there were 40 calls for assistance in the Hunter yesterday.

"There was no wind or storm damage, just a lot of problems relating to flash flooding," he said.

He said the worst hit areas were Hamilton, Kotara and Merewether.

A Weatherzone spokesman said the week's run of stormy days had been caused by a deep and slow-moving trough, fed by a large amount of moisture from a warm Tasman Sea.

He said yesterday's storms were likely the last experienced in the region for this system.

In the wake of the trough, a strong high pressure system will drive cool onshore winds along the coast, producing light showers.

The bureau has forecast isolated showers in the east of the region for Sunday and Monday, but fine weather in the west.