Torrential rain has drenched parts of South Australia and a fresh storm front is now hitting eastern parts of the state.

Kapunda in the state's Mid-Murray has been hit hard with heavy rainfall and the town has suffered widespread damage.

Several shops have been flooded and roofs have caved in.

Flooding was also reported further north at Burra.

Damage has also been reported at Whyalla on the Eyre Peninsula.

A tornado in the sky near Murray Bridge SA. ( Twitter: @curtisashley1 )

The weather bureau said the storm was moving into the Barossa Valley and a tornado had been spotted near Monarto, west of Murray Bridge.

Senior forecaster Simon Timkey said it was not unusual to see a tornado "here and there".

"Tornados are another severe thunderstorm phenomenon, so we don't see very many of them," he said.

"But it's not unusual to see the odd one here and there. Certainly not the size of the big ones that you see images of from the United States at times.

"If you do happen to see one of those you want to make sure you keep yourself in a safe spot, because they can produce some strong and damaging winds."

A severe weather warning for Adelaide has been cancelled, but a severe thunderstorm warning for heavy rainfall, flash flooding, large hailstones and destructive winds remains for much of the state.

SA Power Networks said at 4:30pm about 3,400 customers were without power across the state.

Alecia Jones, from the Kapunda's art gallery, said the rain was so heavy she could not see the buildings across the road.

"It was just white," she said. "The road was six inches under water. It was just a river."

Owner of a clothes shop Lee Sparrow described the downpour as "chaos, mud, water".

"It was a mess," she said.

"Outside looked frightening. I thought the water was going to come under the door."

Jenny Turner from Burra said her lounge room was flooded.

She said water poured through the ceiling and through the light fittings.

"We've got buckets and towels ... and we could almost fill a rainwater tank with what we've got inside at the moment," Ms Turner said.

"I'm sure there'll be people who'll be happy to see the rain but it could have come in a much nicer way."

"I'm just concerned the ceiling might collapse."

"At least I didn't wash the floors this morning like I was planning to."

The town of Kapunda in SA's Mid-North receives heavy rainfall during a thunderstorm. ( Supplied: Joanne Cavanagh )

Other locations that may be affected include Renmark, Port Augusta, Clare, Murray Bridge and Moomba.

The State Emergency Service (SES) earlier distributed sandbags from a number of its depots across Adelaide and regional SA to help residents protect their properties from any rising waters.

Heavy rainfall overnight delivered 87 millimetres at Port Pirie and 57mm at Whyalla.

At the airport at Port Pirie, a downpour of 45mm was recorded in just 45 minutes after 10:00pm on Tuesday night.

Late on Tuesday, heavy rain caused flash flooding at Port Lincoln on Eyre Peninsula as close to 20mm fell in a short time.

Emergency crews had a busy time across the Eyre and Yorke peninsulas dealing with about 180 callouts due to flooding or thunderstorm damage.

Leanne Adams from the State Emergency Service (SES) said flash flooding at Port Lincoln stemmed from a pump failure.

"A pump that usually moves water from an area that's prone to flooding failed, which caused some significant flooding in that area and damage to around 20 different business premises," she said.

The art gallery in Kapunda has been damaged by the storm. ( ABC News: Candice Marcus )

The SES said there was no time to put sandbags in place to protect any businesses because no-one had foreseen the likelihood the pump would fail.

When floodwaters rose around the McDonald's store at Port Lincoln, Tamara Barker decided to have some fun with her kayak.

She said she placed a drive-through order and then paddled around the side of the store to pick it up.

"As I came around the corner after ordering, they all cracked up laughing," she said.

Tamara Barker took her kayak to McDonald's to grab some cheeseburgers. ( Facebook: Hann Barker )

"I don't think they were expecting to see me in a kayak coming around the corner.

"I ordered a couple of cheeseburgers.

"I just thought it was going to be a bit of a laugh. [It's] not every day you get to go down your main street in a kayak."

Ms Barker said flash flooding along that street was above her knees at one stage.

"I've never actually seen it this flooded, but every year we do get a good flooding ... but this year was definitely the worst," she said.

"It was fun to get out in the kayak."

Mr Barker said a lot of local businesses had suffered from the flooding, including her mum's business.

Mike Scarman spent Wednesday morning assessing the damage to his travel agency in Liverpool Street at Port Lincoln.

He said he had been at the premises since 1986 and this was the worst flooding he had seen.

"We've never actually had water up in our office [before], we've had it up to the office but it's never actually got in," he said.

"We were very lucky, the water only went a metre-and-a-half inside the office, on the carpet, but of course all of the low-lying businesses opposite us they have been hit really bad, so I feel sorry for them."

Lightning blamed for blackouts

At Port Pirie, some houses had minor water damage from the downpour, with the SES saying the most common issue was leaking roofs.

About 1,500 properties lost power overnight and SA Power Networks.

Spokesman Paul Roberts said lightning caused the most problems.

"It's the lightning strikes on [power] lines and particularly on insulators — the poles stand pretty tall in those locations and are are a nice target for the lightning," he explained.

Mr Roberts said shattered insulators were quick for emergency crews to find and repair but those that sustained only hairline cracks could take much longer to locate and fix.

He said repair crews were having problems gaining access to some areas because of flooded creeks or other rain damage.

The state Department of Transport said some outback roads were closed after the heavy rain and some others were now passable only to some four-wheel drives and heavy vehicles.

Red marks the SA outback road closures after heavy rain, while other lines show roads passable to only some 4WD vehicles. ( Dept of Transport )

The rain was generally lighter in Adelaide, with less than 5mm recorded at the weather bureau, nearly 11mm in the western suburbs and about 17mm in the northern suburbs. However, Buckland Park on Adelaide's northern fringe had 30mm.

RAA Insurance said spring was a common season for weather-related insurance claims.

"In November we get more than 50 per cent of our annual lightning damage claims and see a high percentage of wind damage claims as well," claims manager Hayley Cain said.

"Electrical storms are really common at this time of year and can cause damage to solar panel inverters and affect electrical equipment following a power surge."

Heavy rainfall filled the streets of Port Lincoln with the town receiving more than 20 millimetres since 9am. ( Supplied: Jacqui Baker )

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