Melbourne's commuters endured 100 per cent humidity, rain and misty skies on Tuesday morning. The sticky conditions were thanks to a night of rainfall across the state, with the town of Strath Creek recording an exceptional 54 millimetres in only 30 minutes.

But meteorologists are most concerned about possible flash flooding, as heavier rain will fall across the city between midday and 9pm.

The state's south-west was drenched on Tuesday morning, with Cape Nelson receiving 41 millimetres of rain, Port Fairy 38 millimetres and Warrnambool 40 millimetres.

"What we had at Strath Creek overnight is entirely possible anywhere over Melbourne today and this afternoon, so that's our concern today," Bureau of Meteorology senior forecaster Stephen King said.

"If it falls in an hour period it could lead to flash flooding in the Melbourne area. Between midday and 9pm will be our period of concern for flash flooding."

In the small town of Yea, next to Strath Creek and about 100 kilometres north-east of Melbourne, the main street of town was flooded, trees fell down and lightning struck the local hospital.

Between 6.30 and 7pm on Monday more than 50 millimetres of rain bucketed down.

Yea Newsagency owner Lynne Bailey said she was at home lifting a tree off her shed, when he found out the shop had been flooded.

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

She said the drains in the street "didn't hold" and then traffic pushed water through the shops.

"I was getting the neighbour's tree off my shed at home, and got the call the shop was flooded," Ms Bailey 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."

Trees fell down all over town, damaging some of the Yea Caravan Park cabins.

Just after 6pm, lightning struck the roof of Yea and District Memorial Hospital.

???"One of my staff was actually in her office, and when it hit she dove for cover, it was so loud," Lorina Gray, hospital director of nursing/manager, said.

Luckily, Ms Gray said the patient care area was unaffected.

"We lost roof tiles, but in the admin building, we're grateful to the SES who put tarp on it last night and the roof was repaired this morning," she said.

The SES responded to about 100 calls for assistance in the Yea area overnight on Monday and into Tuesday morning.

A severe weather warning for heavy rainfall remains in place for much of Victoria, with flash-flooding warnings across the state, including Melbourne, Geelong, Ballarat, Horsham, Warrnambool and Bendigo.

The State Emergency Service has activated the State Control Centre after the flooding, and a spokesman said they were anticipating further damage to some parts of Victoria on Tuesday afternoon.

"We're expecting more later on this afternoon as the low pressure trough moves across Victoria," he said.

"We're guessing that will push through the state around 3pm, it won't reach Melbourne until early evening."

He said this afternoon's storms looked like they would be more widespread than on Monday night.

Mr King said overnight on Monday most of Melbourne received between five and 10 millimetres of rain. At Olympic Park, the measurement area closest to Melbourne CBD, there was 4.4 millimetres of rain between 9am Monday and 9am Tuesday.

"Some areas out to the north-west got a little bit more [rain], and that was associated with thunderstorms. Up around Melton, Bacchus Marsh, Whittlesea /King Lake, there was around 20 millimetres," he said.

"The thunderstorms were in the outer northern suburbs and they weakened as they approached the city last night."

After receiving 54 millimetres of rain in just 30 minutes on Monday night, Strath Creek near Broadford recorded a total of 63 millimetres overnight.

The rain might clear briefly later on Tuesday morning, but then commuters will likely be drenched this afternoon.

"The bulk of the rain is clearing out to the south now, so we might get a clear patch this morning but then we will see showers develop later this afternoon," Mr King said.

"That commuting hour will most likely be saturated."

Humidity shot up to 100 per cent due to the rain on Tuesday morning, but was likely to drop to 70 per cent as the temperature increased.

"When it's raining, it's usually at about 100 per cent, but once the temperature increases later the humidity should drop to 70 per cent," he said.

"There will be showers in the morning tomorrow and they should clear by the afternoon, they'll be much lighter than what we're expecting today."

Melbourne will reach a top of 25 degrees on Tuesday, followed by 22 degrees Wednesday. Thursday and Friday will be fine and partly cloudy, with tops of 24 and 26 degrees.