Melbourne has woken up to a month's worth of rain that has caused flash flooding, downed trees and prompted more than 300 calls to emergency services across the state.

Key points: The flash flooding caused major peak hour delays on public transport

The flash flooding caused major peak hour delays on public transport More than 100 millimetres of rain fell in the Alpine region overnight and at least 57 mm was recorded at Melbourne Airport

More than 100 millimetres of rain fell in the Alpine region overnight and at least 57 mm was recorded at Melbourne Airport Severe weather warnings for the Central, East Gippsland and North East forecast districts have been cancelled

Bureau of Meteorology (BOM) meteorologist Peter Otto said 55 millimetres of rain hit Melbourne overnight — the highest rainfall for March since 1929.

The average rainfall for Victoria in March is 50.1 mm.

Mr Otto said the wet weather was the result of remnants of ex-tropical cyclone Esther moving south from Queensland and the Northern Territory.

A month's worth of rain hit Melbourne overnight, causing flash flooding in the early morning. ( ABC News: Billy Draper )

Heavy rainfall was expected to hit north-eastern Victoria today with possible totals of up to 100 mm.

"Melbourne showers will ease throughout the day and north-east storms will clear overnight," Mr Otto said.

A spokesman for the State Emergency Service (SES) said crews began responding to calls for help in the early hours of this morning as people woke up to the damage.

The SES received 323 calls for assistance between 3:00am and 3:00pm, mostly related to building damage and flooding.

Delays on trams and train lines around Melbourne are clearing after flash flooding led to signal faults and flooded tracks.

Homes, tram lines and train stations flooded this morning as heavy rain continued to fall across Victoria. ( ABC News: Pat McGrath )

Alister Drayton from the SES said he was disappointed that volunteers were called out to rescue 17 people from vehicles stuck in flood waters.

"That's some poor decision making from people," he said.

Power at Richmond Station has been restored after a local power outage affected Richmond and Cremorne.

An Ascot Vale resident woke up to significant flooding due to blocked gutters. ( Supplied )

Earlier delays on the Belgrave, Lilydale and Glen Waverley lines have been cleared.

There are delays and cancellations on the Ballarat line due to a signal fault at Rockbank. No trains are running on the Seymour/Shepparton/Albury line between Seymour and Albury.

Severe weather warnings for the Central, East Gippsland, Northern Country and North East forecast districts have been cancelled.

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The SES has warned people to watch out for unstable trees damaged by heat or fire that could fall in windy or wet weather.

Rainfall run-off into waterways may contain debris such as ash, soil, trees and rocks in fire-affected areas.

The former cyclone hit the Gulf of Carpentaria last week and made its way across to the West Australian coast before making a U-turn and moving back over the Northern Territory, north-east South Australia and south-west Queensland before last night sweeping into Victoria.

"There is a risk of thunderstorms this afternoon but there's no hail with this system. Certainly intense rainfall and damaging winds in elevated areas," BOM senior forecaster Michael Efron said.

The wet weather has also led to a warning about the threat posed by the poisonous death cap mushrooms which have sprouted early this year due to recent rain.

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