Several days of frantic sandbagging is paying off in southern Manitoba as a crest of flood water is expected to pour through the region.

"Thanks to an absolutely incredible mobilization, we have gone from the scenario we saw just a few days ago to the point that we have now almost completed preparations for the crest," Emergency Measures Minister Steve Ashton said Tuesday.

"The next 48 hours are going to be critical."

A torrent of flood water from Saskatchewan is making its way through Manitoba now. The crest passed through Brandon, Man., on Sunday without topping the city's dikes or forcing evacuations.

Manitoba is expecting the Assiniboine River to rise to same levels as the 2011 flood -- one of the worst in the province's history.

The surge prompted Manitoba Premier Greg Selinger to declare a state of emergency Friday and ask for military assistance to prepare homeowners.

Since then, hundreds of military members, reservists, provincial staff and volunteers have been preparing for the high water by making sandbags and shoring up dikes.

Roland Rasmussen, reeve of Cartier, said most of the 60 vulnerable homes in his area were protected and ready for when the crest of flood water is expected on Wednesday.

Downstream in St. Francois Xavier, reeve Roger Poitras said all the homes in his municipality should be OK.

"We feel pretty confident that everything is going to be fine," he said.

"Now, it's just to see how the river handles the flows and if the dikes are going to hold up well. We're confident and we've been told things should work out quite well."

Across the region, about 350 homes are considered vulnerable to the rising water -- 150 of those could flood if the province decides to deliberately breach a dike at the Hoop and Holler Bend to take pressure off the dikes downstream.

Maj. Mike Legace said Canadian Forces members have been working around the clock and making roughly 100,000 sandbags a day, adding to the province's arsenal of one million sandbags.

On top of building up temporary dikes around vulnerable homes, military helicopters are surveying the region and troops have also shored up some weak spots along the province's dikes to prevent a breach.

"We're into our fourth day of the mission. There are a few sore backs but we haven't had any very serious injuries yet," Legace said.

"We're meeting the needs of what the province wants us to do, as best we can do it, and then we'll just start holding our fingers crossed and hope for the best."

The main focus for the government in the coming days is to see whether the dikes and diversion channels hold up against the surging water.

"We are clearly going to be as prepared as possible by noon tomorrow," Ashton said. "We are going to work around the clock to maintain our flood defences."

In Saskatchewan, emergency management commissioner Duane McKay said the forecast "is turning in our favour" as the province deals with the aftermath of heavy rain that fell more than week ago. But he also urged people not use some of the lakes in eastern Saskatchewan.

"We still are quite concerned for some of the safety of the people in particular areas that have seen some of the damages," said McKay.

"We'd remind individuals that there is a lot of debris in the lakes, specifically Crooked and Round Lakes, and so we would caution people using the water there that obviously some of the stuff is partly submerged and could create safety hazards for folks."

The Saskatchewan Ministry of Health also warned people to avoid swimming or bathing in lakes and rivers affected by flooding. It said samples taken in several locations show high levels of E.coli bacteria in the water.

Seventy-four eastern Saskatchewan communities remain under states of emergency and about 230 people were still out of their homes because of flooding.

Nearly 50 people were also to be moved out of the James Smith First Nation near Melfort on Tuesday because of flooding. More rain over the last few days was cutting off access, said McKay.

"They also have significant water accumulations in particular areas, so water's running into those low areas where the road is, so the ambulances, fire engines, police can't get in and out of those particular areas, which creates a bit of a risk for those that have health issues," he said.