The hooked shape made it hard to get out, while the shallow beach shelves were difficult for whales to detect with their sonar, he said.
"When they're swimming, their sonar won't be reflecting back off anything, so they'll probably be getting into shallow waters and into trouble without them realising.''
Otago University marine scientist Associate Professor Liz Slooten said pilot whales were an oceanic species that usually lived in much deeper water.
"When they come close to shore, they are not so familiar with things like coastlines, tides and so on. So that can cause trouble,'' she said.
"That particular area is a real hot-spot for strandings because it's really shallow.''
Pilot whales lived in very stable communities, so when one or two got in trouble, the rest of the pod would not leave. "That's an added challenge.''
Project Jonah chairman Mark Simpson said individual whales stranded if they were sick, injured, at the end of their natural life, or hungry from overfishing.
When large groups of pilot whales stranded, it tended to be because of their close social bonds.
"The rest of the pod follow them in, and we've seen that type of behaviour this week.''
Mr Simpson said strong ocean currents in the Cook Strait at this time of year may have contributed.
"The whales have got a lot of youngsters with them and ... if you're swimming against strong currents, the water on the inside of the spit is slacker, so they would tend to head into that slacker water.
"Their sonar doesn't work very well on sandy, muddy bottoms - they get no bounce-back telling them there's land in front of them.
"They get into Golden Bay and then the tide drops down very, very quickly. When it drops four inches in Golden Bay, all of a sudden there's 7km of mud flats and the whales can't swim out quick enough.''
There was not really anything that could help stop strandings, Mr Simpson said.
"Not unless somebody's going to move Farewell Split.''
Mr Simpson said New Zealand had more strandings than anywhere else in the world, due to its long coastline, sandy beaches, sloping tidal areas, and deep trenches that attracted ocean-going whales.
However, New Zealand's success rate in refloating whales was better than anywhere else in the world.
