The Loddon River has peaked at Kerang in Victoria's north but is expected to remain at major levels for days, while the Murray River as continued its rise at communities around Echuca.
SES Chief Operations Officer Tim Wiebusch said the Loddon River peaked at Kerang at 77.97 metres above sea level, slightly below the 78m which was forecast, on Saturday morning.
"The indications are that we could see flood levels in that 77.7 to 77.8 region for quite a number of days," he said on Sunday.
"Kerang will continue to be isolated for that period of time."
He said 20 homes in the town of about 3,000 people, as well as a caravan park and industrial area, had been impacted by floodwater following a levee breach.
The levee to the western side of Kerang was breached on Saturday, while levees on the eastern side of the town are expected to hold as floodwater gradually recedes.
"We still have a local road in there, but we are advising the general public that Kerang is generally not accessible," Mr Wiebusch said.
Thomas Cove, who runs another caravan park at Kerang, said there had been mixed emotions about the town being cut off and whether residents should evacuate.
"Everyone is feeling a little anxious because you don't know what is around the corner but I think the majority of the vibes are pretty positive," Mr Cove said.
Mr Cove and his wife Amanda moved to Kerang just six weeks ago and said they decided not to leave so they could protect their business.
"When you see flood you think it is just going to be a little one, but when they brought about 20 truckloads of dirt to my property to build up the levee and you hear people comparing it to 2011, you start getting more worried," he said.
But Mr Cove said the community had been united in its efforts to defend Kerang against floodwater.
"Everyone has taken work off and has been willing to help and volunteer and they have all banded together," he said.
Echuca and Moama still waiting for Murray River to peak
The Murray River at Echuca reached a height of 94.8m on Sunday, exceeding the level where it peaked in the 1993 floods that devastated the town.
On the NSW side of the river, the twin town of Moama was experiencing the same event.
Evacuation orders have been issued for the town and its surrounds, with a 2.5-kilometre levee built to protect homes.
An old old levee was breached on Saturday night, with crowds gathering to watch water flowing over the top. Residents and local authorities told the ABC on Sunday they were confident the new levee would continue to hold.
Mr Wiebusch urged residents to evacuate and said the emergency service could not issue a more serious alert.
"We can't emphasise enough, that those levees – while they're holding at this point in time – do continue to be a vulnerability for that community," he said.
"Our advice is to evacuate rather than becoming isolated or impacted in that area."
The river was expected to peak at about 95m on Sunday night or Monday morning.
It is being fed by raging tributaries, including the Campaspe and Goulburn rivers.
Moama Mayor Chris Bilkey said his town's levee was built to 96m and he was confident it would hold.
He said authorities were patrolling the levee, dealing with leaks and were prepared to pump water back if any leaks occurred.
By Sunday, Mr Bilkey said the community had filled over 150,000 sandbags and distributed them around town.
"It's been heartwarming, it's been humbling, to see the community come together in this way," he said.
Further stormy weather expected in northern Victoria
Much of the country is being battered by dangerous weather, with south-east Queensland on alert for flooding after copping a drenching on Saturday night.
The weather system was moving south on Sunday towards New South Wales, where there were 122 flood warnings in place.
Wet weather was expected to continue to lash much of Victoria over the weekend, following heavy downpours on Friday evening.
Mr Wiebusch said Swan Hill further north-west along the Murray was expecting to see major flooding around the first week of November, potentially above the levels reached in the 1993 flood.
He said there could be a return to major flooding in Shepparton and Mooroopna, but only if the upper end of the expected rain totals was reached.
In Rochester, where a man died in floodwater a week ago, Mr Wiebusch said the Campaspe River had returned to minor flood levels, but there could be renewed rises due to rainfall.
"It could impact around 50 properties if we do see that upper end rainfall," he said.
Emergency Management Commissioner Andrew Crisp said there was 30 millimetres of rain on Saturday night in Rochester, but it did not cause flooding.
"It is the reality that we're going to see more rainfall," he said.
"We do still have a major flooding emergency across our state, and we will for quite some time."
The flood event is predicted to continue for four to six weeks along the Murray.
The Bureau of Meteorology's Michael Efron said further thunderstorm activity and rainfall was expected particularly in the north-west of the state.
"Overnight Sunday into Monday, we are expecting that rainfall to extend further south and become more extensive," he said on Sunday.
He said throughout Monday, northern and western Victoria could expect 15 to 30mm of rain.
"The further south and east you head, falls only likely to be around 5 to 15mm," he said.