The children were in a car that was submerged, the Royal Canadian Mounted Police said. The three other people in the car managed to escape.
In a separate incident in the eastern province, a youth and a man were reported missing under similar circumstances, the police agency said.
Heavy rains falling since Friday in Nova Scotia have cut off roads and flooded homes.
Premier Tim Houston told a news briefing that the province had received some 25 cm (10 inches) of rain -- the equivalent of three months' rainfall -- in less than 24 hours.
Houston declared a state of emergency in several areas of the province and urged residents not to join the search for the missing as "conditions remain dangerous."
He estimated that it would take several days for the water to recede.
People in the Windsor region got evacuation orders in the middle of the night because of the danger that flooding would cause the breach of a dam.
But relief valves were opened early Saturday to reduce pressure and the situation is now under control, said Windsor Mayor Abraham Zebian.
News footage and images on social media showed roads that looked like rivers and many cars abandoned in the water.
Environment Canada's weather service said heavy rain was expected into the evening in the eastern part of the province.
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