The province says the river reached its high-water mark on Saturday morning at Brandon, and that it surpassed the level reached during the record-breaking flood that hit the province back in 2011.
A severe thunderstorm warning was also issued Saturday for Brandon, bringing the possibility of damaging wind, hail and intense rain.
Steve Topping with the province's water stewardship department says there likely won't be enough precipitation or wind to increase the flood threat on the Assinboine.
Topping says the intense winds could generate big waves on the province's lakes, which is where the floodwater has been going.
But Emergency Measures Minister Steve Ashton says the current water level on Lake Manitoba is still close to a metre less than it was in 2011.
The province says it has sent 2,000 super-sandbags to the area to prepare for possible flooding.
"These communities have invested, in some cases, in permanent dikes, but there are some properties that are not protected by these permanent dikes," Premier Greg Selinger told a media briefing Saturday.
"We're meeting with these communities as we speak and we are dispatching super-sandbags and support as rapidly as possible."
Topping says the new crest is only expected to raise the water level on Lake Manitoba a few centimetres, but he says that forecast will be reviewed.
On Friday, Selinger thanked the more than 500 military and reserve members who were deployed after he declared a state of emergency a week ago. They set up hundreds of thousands of sandbags, shored up dikes and monitored them for leaks.
The military has begun to pull out of the region now that Assiniboine is falling in most areas and are returning to their bases.
The province said Saturday that the flood forecast on the Assiniboine downstream at the Portage Diversion, which funnels water from the Assiniboine River into Lake Manitoba, called for a crest similar to one earlier this month.
The river rose suddenly last week due to heavy rainfall upstream in Saskatchewan that fell on ground that was already saturated.