Officials say the river is cresting and will remain high for at least 24 hours before the water starts to recede. Emergency Measures Minister Steve Ashton said defences are holding and dikes are being monitored constantly.
Recovery centres are being set up in southwestern Manitoba as the focus turns to cleaning up. But Ashton said that isn't the case for those around Lake Manitoba, where all the water is draining.
"In other parts of the province — particularly with Lake Manitoba, Lake St. Martin and to some degree Lake Winnipeg — (we're) looking ahead to further challenges over the next several weeks and months," Ashton said. "Clearly we're going to be dealing with flooding in Manitoba into the fall. We are taking absolutely nothing for granted."
Lake Manitoba is at flood stage, but officials say the high winds that have caused significant waves and flooding along the shoreline were calming. Ashton said he knows people on Lake Manitoba are anxious, but he said flooding in the region is not as bad as it was in 2011.
The province is moving ahead with construction of a $300-million second channel to help drain Lake Manitoba, but it will likely take seven years before the outlet can be used.
The plan was slammed by residents around the lake who held a rally Tuesday to demand the government take action now.
Tom Teichroeb, chair of the Lake Manitoba Flood Rehabilitation Committee, said their region has bourne the brunt of flooding for the second time in four years.
"This is simply unacceptable," he said in a release. "The best that Mr. Ashton can do is to suggest he will make the residents from Lake Manitoba wait for another seven years. This is utterly irresponsible."
Water coming from Saskatchewan recently prompted Manitoba to declare a state of emergency and call in the military to help with preparations. A first crest moved through the province last week and a second one is now making its way through southern Manitoba.
Just over 600 people are out of their homes, many as a precaution as water overtook roads and cut off properties. Some 43 municipalities have declared a state of emergency.
Steve Topping, executive director of hydrologic forecasting and water management with Manitoba Conservation, said the weather appears to be co-operating at last.
"We have very favourable weather coming," he said. "It looks we're due for sunny skies and minimal winds."