Police searching for a man who went missing while riding a tube down the flooded Todd River in Alice Springs have pulled a body from the water.

Police and emergency services were called to the Wigley Waterhole, a popular swimming spot on the river north of the town, about 6:30pm (ACST) on Thursday.

Watch Commander Pauline Polychrone said the 24-year-old man was with a friend when he got into trouble and went missing.

She said the friend was able to get out of the water and alert police.

Rain has eased in Alice Springs but water is still flooding down the Todd River after heavy rain on Thursday.

The river is usually dry and sandy but it started flowing after parts of the catchment recorded more than 100 millimetres of rain.

It was the first time the river started flowing since April last year.

Sorry, this video has expired Video uploaded to social media shows two other people tubing down the flooded Todd River

The missing man was not the only person to try tubing down the Todd River, with video surfacing on social media of of two other people riding a tube down the flooded waterway.

Royal Life Saving NT executive director Floss Roberts said it was worrying people were ignoring advice to avoid flooded waterways.

"If you continue to swim in flooded waters there's sadly going to be more drownings, so we need to stop this behaviour," she said.

She said it was saddening people had taken to social media to post video of tubing down the flooded river.

"If people are thinking that these [videos] look like fun, remember somebody has drowned in this situation," she said.

Ms Floss said statistics showed 90 per cent of drownings, deaths and permanent injuries in flooded waterways were males aged between 15 and 35.

Rain cuts highway, causes problems on roads

Most roads across the Todd River near Alice Springs remain closed.

Police said the Stuart Highway was impassable at Kulgera, 270 kilometres south of Alice Springs.

The roadhouse and police station had been extensively damaged by flash flooding and police urged motorists to drive with care.

The Todd River is normally a dry riverbed but recent heavy rain has caused it to flow again. ( ABC News: Robert Herrick )

Chris La Page from the Kulgera Roadhouse said a torrent of water smashed through the roadhouse and surrounding buildings at about midnight, leaving a trail of destruction.

"It picked up fridges, freezers and just smashed them up against the wall and yeah drowned all tools and welders and mowers and yeah just smashed everything," he said

A Bureau of Meteorology severe weather warning is still current for people in the Simpson, Lasseter and Tanami regions.

The bureau said thunderstorms and very heavy rain may lead to flash flooding in those areas in Central Australia.

Locations that may be affected include the remote communities of Finke, Titjikala, Papunya, Hermannsburg and Watarrka.

Emergency services are urging drivers to pull over in heavy rain and not drive into water of unknown depth.