Island resident Jane MacDonald told AFP by telephone that she awoke Thursday morning to see "wall to wall seals" and their puppies on four kilometers (2.5 miles) of beaches "decimated" by the storm.
"It was traumatizing," she said. "The seal puppies were literally swept away into the water because their mothers couldn't get them to higher ground."
Mothers nudged their newborn babies to try to keep them afloat. Gray seal pups can swim from birth, but their muscles are weak.
"A wave would hit and the pup went under. The mother pushed it up with her nose, and then another wave would hit. After the sixth or seventh wave, the pup didn't come up," MacDonald said.
"The more you watched, the worse it got. The mothers struggled so hard to save their babies and it just couldn't be done," she said. "I'd never seen anything like that."
Michel Therien, a Canadian fisheries and oceans department spokesman, said "thousands more" seals had landed on a dozen other local islands and Nova Scotia province coasts and suffered the same fate.
He estimates that 75 percent of the gray seal pups born in the region in recent days perished. Many that survived have been orphaned.