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Thunderstorms hit Victoria, as towns in the state's north brace for further flooding

Authorities have warned Victoria is still in the grips of a major emergency as water levels along the Murray River continued rising and thunderstorms caused flash flooding overnight. 

Communities in central and northern parts of the state have been on tenterhooks for days, as gradually rising rivers from rain a week ago slowly swallow homes and businesses.

"We still have a major flood emergency here in Victoria," said Emergency Management Commissioner Andrew Crisp.

There were still 70 warnings across the state at 11:30am on Saturday, ranging from advice messages to the most serious evacuation messages in places like Kerang and Echuca.

Elsewhere in the state, storms and heavy rain returned overnight, with the west seeing the largest rainfall totals.

She Oaks, between Geelong and Ballarat, recorded 78.2 millimetres of rain in just six hours. About 40mm fell in about 30 minutes.

Charlton in the Wimmera region, which experienced emergency warnings earlier in the week, saw about 25mm fall in just 25 minutes.

"Very heavy rainfall across some parts of the state on already very wet ground, so really significant rainfall and thunderstorm activity," Bureau of Meteorology forecaster Michael Efron said.

The SES received 331 calls for assistance in the 24 hours to 6am on Saturday. 

About 100 of those calls were for flash flooding, predominantly in Geelong and Hamilton in the south-west of the state.

Parts of metropolitan Melbourne saw roads and backyards covered in water, with Essendon train station closed on Saturday morning due to flooding.

Echuca hits major flood levels

Mr Wiebusch said by 11:30am on Saturday, the Murray River at Echuca was sitting at 94.77 metres Australian Height Datum (AHD).

That level was where the Murray peaked in the 1993 floods that devastated the town.

A nearly 3 kilometre levee has been built to protect homes, and locals have expressed confidence it will hold.

Mr Wiebusch still cautioned people to heed evacuation warnings.

"We cannot guarantee that the levees will necessarily hold back the waters that are coming down the Murray at this point in time," he said.

Water was seen spilling over an older levee near what is known as Moama Beach on Saturday morning. Locals told the ABC they had not seen that happen since 1993.

The river is expected to peak at about 95.2m AHD on Sunday or Monday.

On the NSW side of the river, the twin town of Moama is expected to experience the same rises.

It is a nervous wait for locals Caitlin Dohnt and Sue Phyland, who came to watch the levee break.

"We're a bit concerned because we're over the bridge in Moama, so if this gets any higher it means people can't get back over to Moama," Ms Dohnt said.

"If this gets up to 96 [metres], the water will be in the town," Ms Phyland said.

"It doesn't matter about the levees, it will just take them out."

For both women, the constantly changing predictions of peak flood levels and times felt like conflicting messaging.

"It’s 94, it’s 95, it’s 96, you’ve just got to come and have a look because you’re not going to know," Ms Dohnt said.

"Seeing this, it feels a bit more real."

The river is expected to stay about that major level for days, before affecting Swan Hill towards the end of the month and continuing on to other townships.

Echuca has been spending the week recovering from the nearby Campaspe River busting its banks a week ago, while preparing for the Murray and Goulburn River's peaks.

Emergency authorities were expecting to see further river rises as a result of the rain on Friday and Saturday, to varying degrees across the state.

The Murray River was not expected to be affected, but the Campapse River that flows to Echuca was expected to rise to moderate levels in the early parts of the week, Mr Wiebusch said.

Chrissy Weller, Mayor of the Campaspe Shire which takes in Echuca, said it had been "all hands on deck".

"We're really at the mercy of it [the water] coming down the river," she told ABC Central Victoria.

Kerang peak revised again, residents given another chance to evacuate

The Loddon River has reached major flood levels in the town of Kerang, about halfway between Echuca and Swan Hill, at about 78 metres.

Residents were on Friday told it was too late to leave, but then on Saturday, when the forecast peak was revised, were told to evacuate immediately if possible.

"Now that the peak has been delayed, people in Kerang are able to evacuate to Swan Hill via one of two routes, depending on their location," said the Vic Emergency warning issued after 12pm on Saturday.

Mr Weibusch said rain associated with the storms may also affect Kerang.

He said even though water levels are expected to be similar to floods in 2011, the town's power station is expected to stay dry thanks to the levee around it.

In the town of Rochester, where a man was found dead in floodwaters last week, the Campaspe River is expected to remain below the minor flood level.

'There is a lot of support available'

Emergency Services Minister Jaclyn Symes said 22,000 applications had been lodged in Victoria for immediate flood emergency payments. 

Both the state and federal governments have made emergency payments available to those affected by the floods.

"There is a lot of support available, the best place to get advice on what is best for you is the 1800 560 760 number. You can be directed to all the support… they'll make sure you know where to go," Ms Symes said.

Ms Symes said she believes all the local government areas affected by flooding should now be on the eligibility list for funding.

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