A man has been found dead near the Brisbane River after being washed away in floodwaters caused by a severe thunderstorm in south-east Queensland.

After earlier hitting the northern Gold Coast and Logan City, the storm moved across Brisbane, leaving more than 4,000 homes without power.

The man's body was found about 6:30pm (AEST) more than two hours after police were called to Eagle Street Pier where it is believed he and a woman were kayaking in drains under the city.

The woman called for help after the water began to swell. The man's body was found 400 metres into an underground tunnel.

After the storm moved through the SES said it received more than a dozen calls for assistance for fallen trees and leaking roofs.

They also freed the occupant of a car that was stuck in floodwaters at Greenslopes.

Heavy rain brought flash flooding to Logan and parts of the Brisbane CBD, before moving north across Redcliffe, Caboolture and Wamuran around 4:30pm.

"It was just a very heavy rainfall thunderstorm," the Bureau of Meteorology's Tony Bannister said.

"The air ahead of it was very, very moist. There wasn't any rotation at all that we look for in a super cell so it was really a more normal type of thunderstorm but it just had very heavy rain in it."

Earlier, about 48 millimetres of rain was reported at Logan Village in the hour to 1:20pm.

At Rochedale and Mount Nebo, 66 millimetres of rain fell in half an hour.

The SES said by 3:15pm it had received 13 requests for help in the Logan area with leaky roofs, sandbagging and trees down.

Major delays were reported on all train lines in and out of Brisbane.

Thousands of ADF personnel and their families who were gathered at South Bank to mark the end of Operation Slipper scattered when the rain descended on central Brisbane.

The rain was so heavy the CBD disappeared from view across the river.

Elsewhere, homes in Chinchilla, about 300 kilometres west of Brisbane, were reportedly damaged by softball-sized hailstones.

Heavy thunderstorms have been forecast across the Darling Downs for Sunday and Monday.

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