There have been 88 flood rescues in the past 24 hours, the majority being people attempting to drive through floodwaters despite warnings not to, frustrating rescuers.
Emergency services repeated warnings for Echuca and Echuca Village residents to leave immediately on Sunday morning after similar pleas on Saturday.
"If you choose to stay, emergency services may not be able to help you," the State Emergency Service said.
Echuca is expected to be hit by two flood peaks, including one by Tuesday and another later in the week.
Earlier on Sunday, people in Murchison, Shepparton, Orrvale and Mooroopna were warned it was too late to leave.
"If you have not evacuated, you should shelter in the highest location possible," the SES said.
The Midland Highway, also known as the Mooroopna Causeway, was slated to close on Sunday afternoon but closed on Saturday evening between Mooroopna and Shepparton.
SES chief operations officer Tim Wiebusch said as the weather cleared, people could be underestimating the danger.
"One of the challenges is we've not got what we call blue sky flooding," Mr Wiebusch told ABC News.
"The rain has stopped ... I think it's more obvious to people when there's heavier rain."
He urged people not to drive through floodwaters.
"That just ties up our emergency services that could be supporting more vulnerable communities that are under pressure with these floods," Mr Wiebusch said.
The Goulburn River at Shepparton rose beyond the major flood level of 11 metres overnight and was expected to peak beyond 12 metres by Sunday night, a record level.
Emergency services had wanted people in Echuca and Echuca Village to evacuate by last light on Saturday, Loddon Mallee incident controller Mark Cattell said.
About 1000 people were impacted by evacuation orders, with around one third in Echuca Village.
Echuca residents were advised to prepare to be away from home for seven to 10 days, with Echuca Village expected to be impacted by the middle of next week with flow-on effects from the Goulburn and Murray rivers.
An emergency warning to move to higher ground was also reinstated on Saturday evening for the Campaspe River downstream of Rochester.
"What we don't want is the Rochester situation where people were comfortable with what was happening, and they were comfortable to stay there, despite us giving them a pretty bleak picture of where it was going to be," Mr Cattell said on Saturday.
"We've spent the last two days evacuating people out of Rochester using boats in some very risky situations."
Authorities predicted about 200 Echuca homes would be impacted by floodwaters.
It was possible Echuca Village could be impacted by the rising Murray River for two or three months, Mr Cattell warned.
A 71-year-old man was found dead in floodwaters in the backyard of his Rochester home in Victoria's north on Saturday, but police were unable to reach the property as it was cut off by floodwater.
Authorities also reinstated an evacuation notice for residents of Charlton on the Avoca River on Saturday and warned major flooding was likely at Appin South along the Loddon River from Sunday morning.
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