Heavy rain began about 5pm on Thursday and bucketed down all night.

The eastern and south-eastern suburbs copped the worst of it, with Rowville recording 66 millimetres in 12 hours.

Bureau of Meteorology senior forecaster Rod Dickson said rainfall totals were about 10 millimetres heavier than forecast throughout the metropolitan area.

The CBD has now recorded 99 millimetres of rain for the month, already far above the December average of 59.

Regional towns such as Echuca and Euroa which bore the brunt of last weekend's record-breaking deluge were spared this time.

Rain did make it as far as South Gippsland and the Warburton Ranges with Mount Donna Buang recording a significant 50 millimetres.

The Bureau issued a severe weather warning at about 7pm on Thursday.

The lashing rain led to reports of flash flooding in Doncaster, Montrose, Toorak, Bentleigh and Pakenham as well as on Dudley Street and Wurundjeri Way in the city.

The State Emergency Service received 216 calls for help between 6pm and 6am, most of which concerned flooding.

Over 60 of the calls were about building damage.

"There were a lot of leaky roofs," SES spokesperson Susan Davie said.

Ms Davie said having clear gutters was one of the best ways to prepare your home for storms.

For those wondering where the season's typical sunny skies are, the downpour does look to be the last of the wild weather.

"It is a very unusually wet start to summer," Mr Dickson said.

"It is going to get warm and it's not too far away now."

After a mild and mostly sunny weekend with the chance of a shower or two on Saturday, the mercury will slowly climb next week to reach into the 30s by Tuesday.