A storm that thundered across Melbourne overnight has created a suburban sinkhole, caused dozens of plane cancellations and brought cleaner air to Victoria after days of choking smoke haze.

Key points: Air quality in Melbourne improved to "moderate" about 3:00am but is expected to plummet to "very poor" on Saturday

Air quality in Melbourne improved to "moderate" about 3:00am but is expected to plummet to "very poor" on Saturday Rain managed to hit some parts of East Gippsland overnight and will continue to cool down the state today

Rain managed to hit some parts of East Gippsland overnight and will continue to cool down the state today The weather saw 130 flights grounded at Melbourne Airport and trains cancelled during Wednesday's peak hour

Almost 600 calls were made to the State Emergency Service (SES) about fallen trees, building damage and flooding on Wednesday.

People were being urged to remain on high alert for falling trees and tree branches, especially in fire-affected areas where the ground and trees had been under stress and were more likely to fall in high winds and rain.

The huge volume of rain also caused a sinkhole to open up in Melbourne's north-west overnight.

The Keilor East sinkhole was initially believed to be 15 metres deep, but that was revised down to a depth of 4 metres this morning.

Kevin Carlisle-Stapleton was the incident controller for Essendon SES last night and said the hole opened up when rain flooded a damaged stormwater drain and swept away soil from underneath the surface.

Emergency services cordoned off the area around the 4-metre sinkhole in Keilor East. ( Facebook: Victoria State Emergency Service )

"A sinkhole is a type of landslide. It occurs when the ground underneath is eaten away through erosion such as an underground stream or a burst pipe," Mr Carlisle-Stapleton said.

He said a resident called in the sinkhole just after 9:00pm along the Steele Creek Trail between Buckley Street and Rosehill Road West.

He said there was no impact to property and no risk of the hole becoming larger.

The sinkhole will be repaired by Moonee Valley City Council.

SES volunteers reassessed the Keilor East sinkhole this morning. ( Facebook: Victoria State Emergency Service )

Severe weather warning for some fire-affected areas

A Bureau of Meteorology (BOM) spokeswoman said 44mm of rain hit Avalon in just 30 minutes last night in a "one-in-100 year event".

The SES urged people to remain vigilant and especially avoid fire-affected areas where trees were weakened in the storm. ( Facebook: Victoria State Emergency )

Rain drenched the city in the early evening, with inner-Melbourne suburbs receiving about 20 millimetres of rain and western suburbs up to 77mm.

When the wet weather did reach East Gippsland it brought little reprieve, with Orbost receiving just 2mm.

Thunderstorms have been forecast across the state's north-east this afternoon.

Between 2mm and 5mm of rain is expected to fall in Melbourne on each of the next few days, followed by another storm forecast to hit the state on Sunday.

Smoke haze to return this weekend

After two days of intense smoke pollution across Melbourne and Geelong which saw ambulance callouts jump and beaches and pools closed, the torrential rain lifted the haze and improved the quality to "good" across Melbourne, Geelong and West Gippsland by midday.

Air quality even improved to "moderate" across the bushfire zone of East Gippsland and the north-east — which had been rated as "hazardous" for days.

An eerie red sunset on Monday heralded two days during which Melbourne's air quality hit rock bottom several times. ( ABC News: Patrick Rocca )

An EPA spokesman said while air quality would slowly improve on Friday, easterly winds would push more smoke across the state over the weekend and bring air quality levels back to "very poor" around Melbourne and Geelong.

Air quality is predicted to drop back to "hazardous" levels across Gippsland and the state's north-east on Saturday.

Severe thunderstorms dumped heavy rain and hail on parts of Victoria clearing the heavy smoke hanging over the city. ( ABC News: Iskhandar Razak )

The EPA is also urging beachgoers to check water quality forecasts before swimming and be on the lookout for algal blooms.

Thirty-six beaches and four sites along the Yarra River have been rated as having "poor" water quality today.

Trains cancelled, planes grounded

Thousands of passengers were left stranded at Melbourne Airport overnight after thunderstorms grounded planes.

Some flights into Melbourne were diverted to Adelaide and Sydney and others were forced to turn back and land in Canberra.

A Melbourne Airport spokesman said 130 flights were cancelled yesterday and overnight and extra flights were scheduled for Thursday to help stranded travellers.

Heavy rain swept across Melbourne yesterday, causing some train services to be cancelled. ( ABC News: Darryl Torpy )

Commuters heading home during peak hour last night were also affected when three train lines were closed due to lightning.

A Public Transport Victoria spokesman said the Mernda line between Parliament and Bell and the Hurstbridge line between Parliament and Heidelberg were both down for three hours after lightning struck near Victoria Park station, causing issues with equipment.

There were also issues between Burnley station and the CBD due to lightning strikes just before 7:00pm.

"This morning everything is looking good. There's no flooding, there are some trains running late due to train drivers driving a tad slower because of slippery tracks," the spokesman said.

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