Environment Canada said some areas in Ontario could get up to 75 millimetres of rain by early Tuesday, while upwards of 45 millimetres of rain was expected in southern and central Quebec.
"The frozen ground has a reduced ability to absorb this rainfall," Environment Canada said in a statement.
"Localized flooding in low-lying areas is possible."
Residents in both provinces have already been affected by overflowing riverbeds.
Several dozen homes and businesses were given evacuation notice on Saturday in the town of Beauceville south of Quebec City, where there was a kilometre-long ice jam along the Chaudiere river.
Police in Laval, north of Montreal, also warned of flooding. The city made sandbags available for pickup at several locations, explaining that a thick coat of ice from the long winter could make things worse.
Pierre Corbin, director of operations at Quebec's Hydro Meteo, said his agency is monitoring several river systems across the province.
"It's rare that you see many sectors affected like at the same time like this," Corbin said.
In Ontario, the City of Belleville east of Toronto is under a state of emergency and many homes were flooded by the rising Moira River, which is up more than 12 centimetres in recent days.
A City of Belleville spokesman said that more than 70 homes had been sandbagged with the help of nearly 500 volunteers, but there were no evacuations forced by floodwaters.
There were fears of even worse flooding in the days ahead, but officials on Sunday sounded notes of optimism and told volunteers they could stand down.
Jennifer May-Anderson, a spokeswoman for local watershed group Quinte Conservation, said rain overnight Saturday wasn't heavy enough to trigger large-scale flooding and that the river hadn't crested like it did in a massive flood six years ago.
"The big question mark had been what rain we would get overnight last night. And the rain that we received last night was not a significant amount of rain so it didn't change things very much," she said.
Environment Canada wasn't forecasting heavy rain upstream the Moira. May-Anderson said a rainfall warning in nearby Bancroft wouldn't lead to flooding around Quinte.
She said the water level, though at a concerning high, should stay stable over the next few days if the amount of rain upstream remains light.
"It looks like things are slowing down and levelling off, but we obviously are not taking our eyes off the situation."
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