Thunderstorms rolled over south-eastern suburbs, dumping 44 millimetres of rain in Narre Warren between 5 and 6pm.

To the west, 57 millimetres fell in Lara, as a slow moving low pressure system from South Australia made its way across the state.

"Hopefully, that should be the worst of it," Bureau of Metrology forecaster Stephen King said.

However, he advised Melburnians to keep their umbrellas on hand on Wednesday morning.

"We'll see showers through the night and into tomorrow morning, but they will be much lighter," he said.

Melbourne looks set to have its second warmest March on record, with temperatures reaching 6 degrees above average.

A high pressure system over the Tasman Sea has blocked any cold front that could have broken the warm spell reaching the state.

"We've had warm, humid air over us and it hasn't budged for close to 20 days," Bureau of Metrology forecaster Peter Newham said.

"It's common to have a cold front come through every four to seven days, but we just haven't had that cycle."

Melburnians will endure several more hot and sticky nights, until the humidity eases with the arrival of a cold front next week.

That cold front could herald the belated start of autumn.

"It will be the first significant change for a couple weeks," Mr Newham said.

Flash flooding

Blue skies briefly returned to Melbourne after an afternoon downpour flooded inner-city streets, including parts of Sydney Road in Brunswick and the junction of Flinders and Queens Bridge streets in the CBD on Tuesday.

Brunswick resident Joanna Stanley was in a clothing store on Sydney Road when rain started falling through the light fixtures.

"Water came dripping through the lights on people who were in the change rooms," she said.

"And then it just got progressively heavier.

"It looks like there's a lake outside. It was quite exciting. I haven't seen anything like this before, and I've lived here for 30 years."

The downpour hit Melbourne's eastern suburbs hardest.

In Mulgrave, water poured through the roof of an IGA store.

At the Mount View Reservoir in Glen Waverly, 32 millimetres fell in 30 minutes.

In the CBD, 7 millimetres of rain fell in just 10 minutes.

Springvale West received 21 millimetres by 3.30pm, Rowville 16 millimetres, Kew 14 millimetres and Oakleigh South 11 millimetres.

The flooding eased almost as soon as the rain did, but shop owners were left mopping up puddles.

Melbourne was set to receive 50 millimetres of rain by Wednesday morning, but the heaviest falls were reserved for other parts of the state.

Warrnambool and Port Fairy, on the state's south-west coast, received average monthly rainfall in less than 24 hours.

From 9am on Tuesday, Warrnambool received 49.2 millimetres, while Port Fairy received 49.6 millimetres.

Yea's main street. Photo: Facebook/Belinda Mcgovern Dean

Elsewhere, the town of Yea is recovering after flash flooding hit its main street and lightning struck the hospital.

More than 50 millimetres of rain hit the town between 6.30 and 7pm on Monday.

Yea Newsagency owner Lynne Bailey was at home lifting a fallen tree off her shed, when she learnt that her shop had been flooded.

"It just bucketed down, it was 15 to 20 minutes of intense rain, it's no one's fault it's an act of nature," she said.

"I came down and I was so lucky, one of my staff was already here.

"The beautiful thing about this community is that everyone jumped in and helped, that's the beauty of a country town."