© Ben SwinnertonLightning lashed Melbourne for two consecutive nights.
Areas northwest of Melbourne received up to 60mm of rain, while the storms also brought down trees and power lines.
Gisborne, about 50km northwest of Melbourne, was worst affected, with the State Emergency Service receiving more than 60 calls for flash flooding.
SES operations manager Tim Wiebusch said extra crews were needed to help clean up.
"The word back we've had from the crews is it's large storm water drains that aren't coping with the downpour,'' Mr Wiebusch said.
"They have had ankle deep water go through quite a few proprieties.''
Emergency crews were forced to close the Murray Valley Highway at Strathmerton just before 1am because of fallen trees.
The road was expected to be reopened within three hours.
The weather bureau said outer northern suburbs like Greensborough and outer eastern suburbs like Croydon and Lilydale were expected to be hit next.
The Melbourne Fire Brigade were called to a Gladstone Park house, which had a small fire in the roof after it had been struck by lightning about 9.30pm.
Lightning also hit a Ringwood home about 10.15pm.
Clarkefield received 60mm of rain in an hour, Jacksons Creek recorded 50mm and Mt Macedon, 40mm.
Weather bureau senior forecaster Phil King said a trough in the northwest of the state was behind the thunderstorms.
"Because it's so humid and sticky we've got a lot of moisture across the state so we're seeing a lot of heavy falls in a short period of time,'' Mr King said.
"The storms will contract across the eastern half of the state tomorrow (Saturday) morning and clear.''
The State Emergency Service received more than 200 calls for help, most between 9pm and 11pm.
Flash flooding hit the fire-ravaged town of Alexandra, with the SES receiving about 20 calls.
"The Commercial Hotel has got three inches of water in it,'' SES operations manager Tim Wiebusch said.
"We also have an aged person's home (where) flooding starting to affect the premises, but people haven't been evacuated.''
Commercial Hotel manager Tanya Rusden said water rushed from one end of the pub, which is famous for its 24 types of chicken parmigiana, to the other and into the main street.
"We tried to bucket the water away, but there was too much of it,'' Ms Rusden said.
"We had to put our staff's safety first and just said, 'Let's just sit back and wait till it subsides'.
"When you stand on the carpet it's like a big bubble is underneath.''
Ms Rusden said the flood had come at the pub's busiest time of year.
"To get this on top of the fires, which were five minutes away, it's a bit disappointing,'' she said.
"I think today (New Year's Day) we did more parmas today (than we've done in a long time).
"There might be a few people who are only up here for a few days who want a parma, but they might have to come back.''
A Ringwood woman was taken to hospital after she received a suspected electric shock.
Her Glencairn Ave home was struck by lightning, causing a small fire in the roof.
When the woman went to touch her bedside lamp, she received a shock.
She was taken to Maroondah Hospital for observation.
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