Emergency warnings remain in place for multiple areas, including Shepparton, Murchison, Echuca, Kialla, Mooroopna, Orrvale, Charlton Barnadown and Elmore.
In Echuca, residents and holiday makers were early on Monday being told to immediately leave amid concerns people could become stranded by the floodwaters.
"Flooding may impact residents whose properties surround the Campaspe River," authorities said.
"Residents in Echuca Village can expect to be impacted over the coming days."
The Goulburn River at Shepparton reached 11.88 metres on Sunday and continued to rise overnight, with major flooding expected when it hits its peak on Monday at 12.2 metres.
That is higher than the 1974 flood level of 12.09m, the Bureau of Meteorology says.
Images show buildings in the middle of town surrounded by a vast inland sea of brown muddy water, and residents using sandbags to protect properties.
The Loddon River at Kerang is expected to peak on Tuesday and into Wednesday, with levels similar to the January 2011 record-breaking floods.
A warning has also been issued for the Wimmera River, with Horsham residents warned major flooding is possible on Monday and into Tuesday.
The Campaspe River at Barnadown, Rochester Town and Echuca had peaked on Monday morning with major flooding occurring - higher than in 2011.
About 9000 residents are currently affected by the flooding with many cut off in their communities amid the rising waters.
The Victorian State Emergency Service has received over 4750 calls for help, including more than 500 flood rescue requests, since Wednesday when heavy rainfall lashed the state.
Prime Minister Anthony Albanese said many people were doing it tough.
"It's heartbreaking to think that for many people this is the third or fourth time in 18 months that their lives have been disrupted by a natural disaster of this magnitude," he said of the floods that swept across Victoria, NSW and Tasmania in recent days.
Emergency Management Commissioner Andrew Crisp said it had been a challenging week with "devastating impacts".
"However, with (more) major flooding expected, it's vital communities, especially in at-risk locations, listen to the advice of emergency services and stay up to date."
More than 7500 properties across Shepparton, Mooroopna, Kailla and Echuca could be impacted by the rising waters, according to modelling.
Disaster recovery payments have been made available to residents in 23 local government areas and a 250-bed camp for displaced people will be opened at the former COVID-19 quarantine facility in Mickleham.
But unlike when the centre was a quarantine facility, residents will be free to move around and socialise with each other, and come and go as they please.
Each room comes complete with toiletries and other necessities, and residents will be provided with three meals each day, and snacks and drinks on arrival.
Charities will provide assistance with items like clothing that families may have had to leave behind or lost during the floods.
About 100 ADF personnel have also been deployed to help with evacuations and sandbagging in the worst-hit areas.
Major flood warnings are also in place for the Broken, Avoca and Loddon rivers, and the Seven and Castle creeks.
The Avoca River could peak aruond eight metres on Monday morning around Charlton.
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