The warning, issued Tuesday afternoon, stretches from St. Lazare to Griswold.
The province says outflows may change as melting and run-off in the upper Assiniboine River basin resumes.
Meanwhile an overland flood warning remains in effect for much of southern Manitoba.
The province says the warning extends from the Saskatchewan boundary eastward to Highway 12 and from the United States border north to the Trans-Canada.
A high water advisory has also been issued for the Whiteshell lakes area as levels on most lakes continue to rise due to rainfall and snowmelt from two late season storms over the past few weeks.
Winnipeg was hit with 70 millimetres of rain over the weekend. Underpasses were flooded, prompting several roads closures. Closer to the United States border, Altona received 76 millimetres, Environment Canada said.
St. Adolphe, a small community just south of the capital, started extending its dike to keep the water at bay.
In western Manitoba, cooler temperatures made for thick, heavy snow instead of rain. Combined with wind gusts of more than 80 km/h — 100 km/h in Brandon — the weather system broke wood utility poles and brought down power lines.
The province says southern Manitoba basins, including the United States’ portions of the Red, Souris, Pembina and Roseau river basins, have received an average of 60 mms of precipitation since April 22.
Cooler weather was expected to slow the melt and temporarily reduce the threat of major flooding, the provincial government said over the weekend, although temperatures are forecast to climb later in the week.
— with files from The Canadian Press
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