The two volunteer firefighters, Christopher Lavoie, 23, and Regis Lavoie, 55, were helping evacuate residents near Baie-Saint-Paul when they went missing Monday afternoon.
Torrential rains following the spring thaw prompted alerts about flood risks across the province this week.
Quebec provincial police spokesman, Sergeant Stephane Tremblay, told AFP that around 10:00 am (1400 GMT) a police helicopter "located a body" in the area.
"We don't have a formal identification yet; this will have to be done by the coroner's office. But everything indicates that it is one of the two people who went missing in this area on Monday," he said.
Later in the day, police said they had found a second body near where the first was recovered.
"Around 1:00 pm, there was a second body that was located," Sergeant Beatrice Dorsainville said.
Flooding washed away several roads and bridges earlier this week, stranding residents of the town of Baie-Saint-Paul, about 100 kilometers (60 miles) northeast of Quebec City, and others.
A half-dozen communities across the province have declared emergencies due to flooding, while others are bracing for possible devastation.
The two firefighters, who are not related, had been in an amphibious all-terrain vehicle (ATV) when it capsized, Marylou Lavoie, the daughter of Regis Lavoie, told public broadcaster CBC.
"My dad tried to hold on to a tree, but it didn't work," she said, recounting what she'd been told by authorities. "The (ATV) hit him and the current took him."
"It's infinitely sad," Quebec Premier Francois Legault told reporters of the loss of life while touring the flood damage.
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