The pups dip and dive in the waters, especially between April and September, with breeding season taking place during the spring and summer months.
The seals, which cross the road at Oahu Point and make their way upstream to the waterfalls, are a global tourist attraction.
But after the quake, rubble spilled across highways and onto shorelines badly damaging the specially protected seal sanctuary.
"It's too soon to be able to know the full impact that the earthquake will have had on the local population," Department of Conservation science adviser Laura Boren told the New Zealand Herald.
"Some seals would likely have been out at sea foraging and so may not have been impacted by this or other slips.
"There are still places north and south of Ohau point where seals can still haul themselves out to rest."
But according to local teen Jackson Lidgard, whose family home is just 5km from the Ohau Point, the seals seem to be doing OK. They're usually more scarce up at the waterfall at this time of year, because the baby seals are too young right now to make their way up there.
"The falls are remarkably undamaged," 18-year-old Lidgard, who also works with Seal Swim tours in Kaikoura told news.com.au.
"The pool and waterfall that the seals swim in is still there. The rubble will clear out in the next rain, and the baby seals will be able to get back to their spot soon enough."
Lidgard, who was knocked to the ground during the quake, lives at home with his sister Harriet and their parents Chris and Annmarie. He said that although there are no seals at the waterfalls, he has spotted a fair few on the shoreline nearby.
"The ones on the beach looked a little lost," he said.
"There were a few on the beach, but nothing at the pool. Luckily it's the time of year that seals aren't up in the waterfall too much.
"There's been people checking in on the seals, but they are pretty self reliant. We try and leave them to their own devices - and so don't interfere with them too much."