All 4,000 residents of the town were ordered to evacuate as flooding reached the community's downtown area, according to the Associated Press.
Chief April Martel of Katl'odeeche First Nation issued the order on Wednesday, telling community members to head south to the town of Enterprise to escape the flooding, which is the worst the region has seen in decades.
Another nearby city, Yellowknife, opened an evacuation centre for people fleeing Hay River, and the Big River gas station in Fort Providence assisted evacuees throughout the evening.
Reports suggest some of the residents leaving Hay River are headed to northern Alberta to ride out the floods.
"Some had very little warning and had to react quickly to stay safe, while leaving their home, their possessions and, for some, their business to endure the water and ice," Northwest Territories Premier Caroline Cochrane and Municipal Affairs Minister Shane Thompson said in a statement on Thursday.
The flooding prompted the regions Department of Infrastructure to shut down the only road leading to Hay River's Vale Island, where the area's airport is located, cutting off air travel to and from the town.
The town sits at the mouth of the Hay River in what is essentially a small delta where that river feeds into the Great Slave Lake. Ice jamming the channel had blocked water over the weekend and heavy rain and snow fall added more water into the system until it ran over the riverbank.
"There was a large volume of ice, a large volume of snow in the basin over winter, and then this storm hit — initially as rain, which then flowed directly into streams and creeks, bumping up the water level immediately — and it parked over the entire basin," territorial hydrologist Shawne Kokelj told the AP. "Now what we're seeing is there's still high water coming from farther upstream because a lot of rain fell there, too, and now some of the snow is melting and so keeps feeding a lot of these smaller streams."
As the flooding continues, officials in cities where evacuees have fled worry for their wellbeing.
According to the mayor of High Level, where many evacuees have taken up temporary residence in hotels, many people are running out of food.
Crystal McAteer, the mayor, said that it was a "huge influx of people for our small community."