Rain has lashed the city, the largest in the province of Quebec, since early on Friday, causing the worst flooding in decades.
The measure, covering four districts, was declared on Sunday afternoon and will remain in place for 48 hours, officials said.
More heavy rain is forecast and the area under state of emergency could be expanded.
They warned it would take several days for the situation to get back to normal.
The order gives the city the power to more effectively and quickly address the situation – including forcible evacuations of residents in some areas.
Nearly 200 people have already been evacuated from their homes. And patients at the Sacré-Coeur Hospital were transferred to a hospital on higher ground as the waters rose.
Pina Bissi, a single mother rescued with her son and dog from the district of Pierrefonds-Roxboro, said: “I’m heartbroken. This is so sad.
“What are these families going to do? What am I going to do?”
More than 140 towns across the whole of Quebec, in Canada’s east, have been devastated and the situation was expected to worsen on Monday as more heavy rain is forecast.
The Canadian Army has been sent with 1,200 troops deployed alongside police and firefighters to help evacuate people – even those desperate to stay and try to save their homes from the rising water.
The town of Rigaud, west of Montreal, has been particularly hard hit.
Mayor Hans Gruenwald Jr said: “People had to be evacuated, and we put them in boats and they are crying like babies.
“I am sorry, they are at a point where now they are not in a position to decide any more their own future.”
In the city of Gaspé a man and two year old child are thought to have drowned when their car was swept away as a river burst its banks on Sunday evening.
A woman managed to escape the vehicle and cling on to a branch but her husband and toddler were trapped.
The flooding is not limited to Quebec, and unusually high rainfall has also caused flooding in the province of Ontario.
Lake Ontario has reached a water level not seen since 1993.
Warmer temperatures have also caused snow to melt in British Columbia in Canada’s west, combining with the rain to cause flooding and mudslides.