The 1993 level of 94.77 metres above sea level was exceeded at the town on the Victoria-NSW border on Saturday night and was expected to peak around 95m overnight.
More rain is forecast for the flood-hit state as a low pressure system moves over northern Victoria on Sunday.
The state's northeast and far northwest are tipped to cop the brunt of the falls and the Bureau of Meteorology predicts the system will bring wet weather to southern Victoria early in the week.
At Echuca, authorities warned anyone left in the area to leave after water spilled over a levee near the centre of town on Saturday.
Despite a makeshift dirt levee in the town holding, Premier Daniel Andrews said some residents were heeding the advice and pleaded with others to consider following suit.
"People give that very careful thought. We don't issue those warnings lightly," he told reporters on Sunday.
About 50 people from flood-hit communities across the state have taken refuge at the Mickleham quarantine centre, Mr Andrews said.
More than 65 flood warnings remain active in Victoria.
Kerang residents are advised to evacuate amid fears flood water might not recede for a month or more.
"We've got water coming in from everywhere," Gannawarra Shire Mayor Charlie Gillingham said on Saturday.
A major flood warning remains current for the Loddon River from Loddon Weir to Kerang after up to 35 millimetres of rain was recorded in the upper Loddon catchment in the 24 hours to 10pm on Saturday.
Further rainfall is forecast for the area over the next few days.
Meanwhile, in the state's southwest, the State Emergency Service received about 140 requests for help from Geelong to Hamilton.
Three people were rescued after driving through floodwaters near Geelong.
The SES has received more than 8300 calls for help since the weather emergency began and more than 750 flood-related rescue requests.
Australian Defence Force personnel have been deployed to assist with preparation, including sandbagging at Barmah along the Murray River and Swan Hill.
Flood warnings remain for towns along the Loddon, Goulburn, Campaspe, Avoca, Barwon, Kiewa, and Ovens and King rivers.
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