A wind alert is in effect for the south basin of Lake Winnipeg today as powerful northwest winds are expected to buffet the shoreline.
On Wednesday, the province urged cottage owners to take precautions. It said boat houses and docks may be at risk.
Manitoba Infrastructure said lake levels could rise three to five feet. Strong winds are expected to last for up to 12 hours.
The situation will be less severe on Lake Manitoba, where winds could raise levels by two to three feet on the southeast shore and one to two feet on the south shore, officials said.
Lake Winnipeg was at 715 feet above sea level Wednesday -- the top of its regulated range.
"Around Lake Winnipeg, we're not anywhere near what we would consider the weather bomb of 2010 (which caused significant property damage), but nonetheless (the) very high wind... will create a high wind set-up and wave action," said Steve Topping, executive director of hydrologic forecasting and water management.
Meanwhile, the province asked the federal government Wednesday for permission to reopen an emergency channel, built and first used in 2011, to drain Lake St. Martin, which is expected to reach flood stage by June 26.
The province served notice to Ottawa on May 28 the emergency outlet may be needed. On Wednesday, it followed up with a formal letter.
Infrastructure Minister Steve Ashton said he was to speak with three federal cabinet ministers late Wednesday to discuss the situation. Manitoba requires permission from Ottawa to operate the emergency outlet, which drains water into Lake Winnipeg.
Heavy rain throughout the spring in several areas of the province have caused lake levels to rise and farm fields in western Manitoba to flood.
Lake Manitoba, which drains into Lake St. Martin, has also been a concern, although it's still 0.7 feet from flood stage.
Lakes in the Whiteshell had been abnormally high, although they've receded in recent weeks. Up to 80 millimetres of rain is forecast for Lake of the Woods in the coming days, which could prompt the Lake of the Woods control board to approve a maximum discharge from the lake. The last time that happened was in 2005.
In western Manitoba, the Shellmouth Dam is full. Some 25,000 to 30,000 acres of Assiniboine Valley land below the dam are unlikely to be seeded to traditional crops this year due to flooding, Topping said.
Manitoba is concerned about illegal drainage by southeastern Saskatchewan farmers, which is having repercussions for southwest Manitoba producers.