The State Emergency Service (SES) is warning much of the State will be hit by damaging winds on Thursday morning.
Wind gusts of up to 110 kilometres an hour will buffet areas stretching from East Gippsland to the Wimmera region.
Flash flooding is also possible in parts of the Northern Country, North Central and North East districts later this afternoon.
Lachlan Quick from the SES says people should be mindful about parking cars under trees.
"With these ones, we're going to see trees down over roads, building damage, trees down into buildings.," he said.
"But there's also going to be warm air meeting up with cold air as this cold front comes through, which means some pretty significant thunderstorms as well.
"So please don't park under trees or take shelter under trees if you're out and about.
"Secure any objects around your property if you can and as always, never drive through flood waters if you get stuck in that sort of element."
Melbourne is also bracing for strong winds and is expected to have a top of 21 degrees.
© ABC 2013
17:45 EST It's been a wet and wild 48 hours in parts of Western Australia with some parts of the grain growing region receiving over 65 millimetres of rain and wind gusts of almost 100 kilometres an hour.