Melbourne gets month's worth of rain overnight

A month's worth of rain has fallen on Melbourne overnight, causing peak-hour chaos and more than 100 calls to emergency services for help across the state.

Melbourne has recorded more than 54 millimetres of rain in 24 hours, which is about how much it usually receives for the entire month of March, with the wet weather bringing down trees, causing damage to homes and flash flooding.

The State Emergency Service has received about 150 call outs for help just before 9am on Thursday, with 50 relating to flooding, 40 for building damage, 29 trees down and 10 rescue requests.

They expected more calls as people woke up this morning.

On the public transport network, trains are resuming on the Hurstbridge line after earlier flooding closed it between Heidelberg and Clifton Hill and on the Sandringham line between Sandringham and Elsternwick.

Burnley Station is experiencing significant flooding on the subway, with plumbers currently on-site.

Multiple roads are also flooded and the wet conditions have resulted in crashes and heavy delays.

Drivers are asked to exercise extreme caution and never drive through floodwater.

The downpour was the result of ex-tropical cyclone Esther moving from the north of the country to southeast, though it was not expected to make it to Melbourne.

"It is particularly unusual because usually these sorts of troughs weaken out before they make it this far south," Bureau of Meteorology duty forecaster Miriam Bradbury told AAP.

"They generally move east or die off, but this one has moved down to the southeast, so that's why we're getting tropical moisture and humidity."

The rain is forecast to ease in Melbourne in the afternoon but the state's east will continue to receive heavy rain, she added.

A severe weather warning is in place for the northeast of the state.

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