The two children had been in a vehicle that was swept away when its occupants tried to flee their home Saturday in the province of Nova Scotia.
Three months' worth of rain fell in a matter of hours over the weekend, washing out vehicles, bridges and roads.
"They were leaving their residences trying to get to a safe area and that's when they were struck with the storm surge," a Royal Canadian Mounted Police (RCMP) spokeswoman said.
"They were leaving and were kind of pushed off of the road into a field that then quickly flooded with water."
Three other people in the car managed to escape.
Rescuers found one of the children on Tuesday and the other on Monday, the RCMP said.
In a separate incident, a man and a teenager disappeared under similar circumstances. The body of the 52-year-old was found Monday, and the teenager remains missing.
The regional municipality of Halifax, the province's capital, said Tuesday that the water was finally starting to recede, though some areas were still flooded.
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