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Dozens of SES rescues as Victoria is hit by flash flooding from overnight rain

Victoria has been hit by widespread flash flooding and dozens of people have had to be rescued after heavy rainfall across parts of the state overnight.

People in Mount Martha, Mornington, Hastings and Dromana on the Mornington Peninsula were told to stay indoors due to the risk of flash flooding.

Residents of Beaufort and Lexton, north-west of Ballarat, have also been warned to stay indoors because of flash flooding.

In an afternoon update the State Emergency Service said it had responded to more than 780 calls, with the spike coming in the early hours of Monday morning.

There were 56 rescues by Monday morning.

The Bureau of Meteorology said storms from the north-east delivered 147 millimetres of rain at Mount Hotham and above 100mm in many areas of the north.

But meteorologist Christie Johnson said it was the slow moving storms that moved in from the west of the state that caused the most damage. 

She said the system intensified as it moved over Port Phillip, causing flash flooding across the Mornington Peninsula.

A wet awakening for Mount Martha residents

Corey Ablett slept through the torrential rain, as well as his family's Mount Martha house filling with floodwater, sewage and stormwater.

The first he knew of the devastation was when he woke up and stepped into a pool of water.

"I get up, walk out of my room and it was just in the whole house," Mr Ablett said.

"The floor boards were up, the carpet was up, everywhere I was stepping was filling up with water."

He quickly turned the power off and looked out to his neighbourhood and saw the water lines on nearby vehicles.

"We've just called some family members, they called their family members and everyone's just come through, a little community, it's quite beautiful, everyone just helping each other out."

The family will shelter with relatives tonight because they fear the rain will return.

"None of really know where we're going to go from here, we're just stuck in a bit of a pickle."

Anita Weaver woke to gurgling noises and dirty water pouring out of her toilet and sinks.

The water quickly spread throughout her home.

"I woke up to a gushing river at five o'clock this morning," Ms Weaver said.

"The water came that quickly and that fast."

She said she found her dog hiding under the kitchen table in distress.

"Now I've got this lovely mess to look forward to and hopefully insurance won't be too long in getting to us to help us because I know other people are in the same boat."

She said she would move in with her daughters while the insurance assessment is carried out.

"Hopefully this will be sorted, I don't know how, it's pretty revolting. Everything is noticeably damaged."

Authorities warn heavy rain will cause flooded rivers to again rise in the state's north.

The State Emergency Service's Chief Operations Officer Tim Wiebusch said the flash flooding at Mount Martha and the surrounding areas caught a lot of people off guard.

"When we see these flash flood events, our stormwater systems quite quickly become overwhelmed and we can actually see what we call back surge occurring in those areas," Mr Wiebusch said.

"So it may be that whilst the heavy rainfall is going into the stormwater system in one location, it can then come out in another location. Some flash flooding we will have seen the last 24 hours will have been as a result of the phenomena."

Flooding closes highways, disrupting travel and freight

The flash flooding has caused disruptions on some major roads.

The Hume Freeway is closed northbound between Benalla and Chiltern, while the Murray Valley Highway is closed between the Hume Freeway and Rutherglen.

A freight train also derailed at Inverleigh, west of Geelong, where heavy rain also fell overnight.

No injuries were reported after a train derailed at Inverleigh, west of Geelong.

The Department of Transport's Chris Miller said the closures meant it was difficult to travel directly into New South Wales.

"If you are headed to NSW, the detour is huge. You need to go via Shepparton, Strathmerton, Tocumwal, Griffith, then Yass, back to the Hume and you obviously need to allow plenty of extra time for that journey," he said.

"The Department of Transport is doing an credible job to reopen roads as best they can under very trying circumstances, said Emergency Management Victoria commissioner Andrew Crisp.

"We'll continue with the Department of Transport to do what we can to ensure that we maintain that connection with our neighbours interstate."

Authorities have now expressed concern about the heavy rain causing flood levels to again rise in the Murray River, in the state's north.

Some other communities along the Kiewa River, Tallangatta Creek, the Mitta Mitta River and on the Murray River downstream from Hume Dam have been advised to move to higher ground.

A minor to major flood warning is in place for the Murray and Edwards Rivers in the state's north and north-east.

Mr Wiebusch said the focus would be on communities in the state's north-east as river levels rise.

"We're expecting a range of river systems in the north-east of the state to reach moderate, if not major, flooding. We saw major flooding at the Murray River at Albury-Wodonga overnight."

Meteorologist Christie Johnson said more showers and storms were forecast across the north on the weekend but, but she said they would not be as severe.

"This looks like moving into the state, this next system, on Saturday afternoon and then affecting central and eastern parts on Sunday," she said.

"But the good news, at this stage, is we're looking at rainfall totals mostly around 20 to 40 millimetres on Sunday through the north-east, maybe isolated falls of 50 millimetres with thunderstorms, but nothing like the 100-150 millimetres that we saw over the last 24 to 36 hours."

Meanwhile further south, he said the Barwon River is also expected to peak at Geelong tonight.

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