Several highways are closed because of flooding and a man has died after being hit by lightning after storms hit South Australia's Mid North and Riverland last night and this morning.

Emergency services were called to a rural property at Eba, west of Morgan, about 5pm yesterday after a 29-year-old man was hit by a bolt of lightning.

Police say he died at the scene.

They will prepare a report for the coroner.

Storms passed through the area on Saturday and Sunday.

The highest rain total was 60 millimetres at Robertstown.

Cooinda, near Blanchetown, received 49mm of rain in six hours on Sunday morning, while 46mm fell at Mount Mary.

Saddleworth in the Mid North received 43mm of rain in six hours and Freeling, north of Adelaide, recorded 38mm.

The Thiele Highway is closed at Bower.

The Worlds End Highway has reopened after earlier being closed north of Robertstown, while the Barrier Highway has reopened after earlier being closed at Manoora.

The State Emergency Service has issued a watch and act warning for flooding at Stockport, on the Gilbert River, and a broader flood advice warning for the Light and Gilbert rivers.

It is urging people not to drive through floodwaters and to stay indoors until the worst of the weather passes.

The Bureau of Meteorology (BOM) has issued a severe weather warning for heavy rain in the Riverland, the Murraylands and the Mid North today.

It has warned flash flooding may occur.

"With moisture being brought down from the north of the country and with a low-pressure system moving across, the combination of those things is enough to produce some pretty significant rainfall," BOM senior meteorologist Simon Timcke said.