Evacuation warnings are in place for people in Echuca and other towns along the river, with the Murray expected to peak from Wednesday.
Emergency services are concerned river levels could exceed the 94.77 metres recorded in Echuca during the 1993 floods.
People in the northern Victorian town spent most of Monday building a makeshift sandbag levy to protect thousands of homes and businesses.
More than 1000 Echuca properties were already inundated with floodwaters on Sunday after the Campaspe River broke its banks.
There are also concerns the rural town of Kerang, about 95 kilometres northwest of Echuca, will become isolated due to floodwaters.
Major flooding at Kerang along the Loddon River is expected overnight on Tuesday and into Wednesday, with the water forecast to peak around the January 2011 level soon after.
A sandbag levee is expected to help keep the majority of the town dry but it could be cut off for up to seven days, Victoria's State Emergency Service warned.
A warning has also been issued for the Wimmera River, with Horsham residents told major flooding is possible on Tuesday.
With the crisis growing, the federal government on Tuesday expanded the one-off, non-means tested disaster recovery payment of $1000 per adult and $400 per child to the Benalla, Boroondara, Central Goldfields, Greater Bendigo, Loddon, Moonee Valley, Mount Alexander, Murrindindi and Yarra local governments.
The assistance was already open to those in the Campaspe, Greater Shepparton, Maribyrnong, Mitchell and Strathbogie councils.
Other Victorian towns are moving to the clean-up phase, with the state government on Monday announcing a $351 million flood recovery package.
The disaster funding includes $165 million in emergency road fixes such as filling potholes and repairing surfaces to get people and freight moving.
Close to 13,000 people have applied for state relief payments, with almost 4000 people already receiving support.
The state government also confirmed fees would be waived for those trying to remove flood waste.
Residents in 46 local government areas across the state will have their fees covered through to December 31 this year.
It is projected 300,000 tonnes of waste will be sent to landfill as a result of the floods.
In Maribyrnong in Melbourne's west, the council will start collecting hard rubbish that has been strewn across nature strips.
The council spent most of Monday clearing debris and mud from roads and drains after dozens of homes were inundated by floodwaters.
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