The hatchery's staff has been working to move specialized equipment to higher ground and secure potential contaminants since the flood hit Sunday, the Anchorage Daily News reported.
Several outbuildings were swept away during the flood and a bridge that connects the hatchery to a nearby highway was destroyed, said manager Gary Martinek.
No damage estimate had been released.
"It's not the materials, it's the land loss we're really worried about," he said.
Just hours before the river flooded, about 10 million sockeye fry were airlifted to nearby Crosswind Lake, where they joined the wild population.
Martinek said if hatchery workers had waited a day more, none of the fry would have survived.
"All those fry would have died," Martinek said. "You couldn't have put them in the water."