The authorities have turned off the power and moved staff out of the facility because high water was threatening he electrical outlets and panels.
The federal Department of Fisheries and Oceans spokesman Brian Thompson told the media that it was premature to say how much damage could be done, but he added that the water had not broken into the administration building.
"This won't affect the young fish unless there is a lot of silt in the river water," Mr Thompson told the Daily Gleaner.
"We are monitoring conditions at the biodiversity station from across the river at the rearing station," he said.
High Water Closes Hatchery
CANADA - High water has closed the Mactaquac Biodiversity Facility in Canada, although authorities say there is no imminent risk to fish stocks at the hatchery.