Wild weather described as a "cyclone" is expected to hit South Australia this afternoon, with flood watches in place across the state.

Bureau of Meteorology (BOM) regional director John Nairn said the state needed to be prepared because it was "going to get a bit of bang out of the trough that comes through before the low arrives".

"This is a [mid-latitude] cyclone," he said.

"It's a clockwise rotating system and in its own right it's a powerful system, and not to be confused with tropical cyclones."

The "vigorous cold front" was expected to hit the West Coast near Ceduna at about midday, with waves of up to 11 metres expected to batter the coast.

"What we've got with this event this afternoon is a trough approaching and we get a vigorous line of thunderstorms and rain," Mr Nairn said.

Rain and thunder has already arrived on the Yorke and Eyre peninsulas, as well as in Adelaide, as heavy cloud associated with the system rolls across the state.

The BOM has issued a severe thunderstorm warning, saying the system is likely to produce "damaging wind gusts in excess of 90 kph" in the afternoon in the upper Eyre Peninsula and North-West Pastoral district.

It also issued a severe weather warning for damaging winds for the West Coast and parts of the Lower Eyre Peninsula, Eastern Eyre Peninsula and North West Pastoral districts.

"Strong to gale-force west to south-westerly winds averaging 50-65 kph with gusts about 90-100 kph are expected to develop behind the front during Wednesday," a bureau statement said.

"These winds may cause damage to trees and property.

"Following the front, an intense low pressure system will move across the Bight towards the SA coast with strong gale-force winds impacting western parts.

"Wind speeds will increase later today to 50-75 kph with gusts around 90-120 kph, most likely near coasts with squally showers and thunderstorms."

The intense low pressure system forming below South Australia. ( Supplied: Bureau of Meteorology )

BOM senior forecaster Vince Rowland said the worst of the winds would hit Eyre Peninsula and the mid north.

"If the low does track a little bit further south, that could all change so the bureau is monitoring that quite carefully."

Powerful winds are expected to hit Adelaide in the early evening, with between 50 to 100mm of rain forecast for the Mount Lofty Ranges.

A flood watch was in place for the Mid North, Mount Lofty Ranges and Adelaide Metropolitan District.

The storm rolling into Whyalla on South Australia's Eyre Peninsula. ( Facebook: Eric Brokken )

The BoM warned there was a risk of rapidly rising water levels and flooding in creeks and rivers across the watch area, in particular the Mount Lofty Ranges from this afternoon.

It comes just two weeks after homes across the Greater Adelaide area were flooded by burst rivers and creeks.

BoM forecaster Mark Analak said he had never before seen such a forecast for SA.

"It's a big one, I must say I've been forecasting here in Adelaide for the best part of 15 years and I can't recall wind strengths around a low pressure system moving onto the coasts of this strength," he said.

The bureau said towns in country SA that could be affected included Ceduna, Coober Pedy, Wudinna, Elliston, Woomera and Tarcoola.

State Emergency Service chief executive Chris Beattie said significant power outages were expected.

"There is absolutely no doubt there will be powerlines down and SA Power Networks crews will be stretched with this event," he said.

"This is one of the most severe weather events this state has faced in recent history."

The State Emergency Service (SES) said volunteers had handed out about 43,000 sandbags over the past two days.

John Carr from the SES said crews would be stretched to the limit if the intense storm hit was as damaging as expected.

"Once this storm hits our guys are going to be be flat out dealing with a whole range of incidents, not least of which will perhaps be some flooding events, lots and lots of trees down with the winds," he said.