Why are gray whales dying in San Francisco's waters? US scientists search for clues

"It's sad to see a dead whale. It's sadder to see a dead whale that you may have recognised from studying that particular whale. But there's also a lot that we can learn," said Kathi George, whose team assisted Slaathaug with her research and several necropsies - animal autopsies.

Whales, she said, can be harbingers of bigger changes under the surface of the ocean.

That the whale sightings and strandings have begun earlier in the season this year - beginning with two in January when peak numbers are usually in April - is a cause for concern, indicating that the creatures are in more trouble than initially thought.

Slaathaug and her colleagues have also seen very low calf counts, signalling a low birth rate. That could mean this population is neither recovering nor rebounding in the way that it has in previous times of population decline.

"That, in combination with the high rate of human-caused mortality in this area, really leads scientists to be concerned and look for ways to find solutions," Slaathaug said.

Moe Flannery, a co-author of the study, told the BBC that this is the first time in decades where the problem seems immediate. She says scientists are learning how to make the waters from Alaska to Mexico safer for the whales.

The population of gray whales that hug North America's west coast is not considered endangered. However, their numbers have dropped from 27,000 in 2016 to 12,500 in 2025 - a decrease that the US National Oceanic and Atmospheric Administration has dubbed an "unusual mortality event".

"It's an immediate crisis that needs to be addressed and this paper is just the first step in gathering the science that's needed to help inform conservation and management of this species that's in trouble," Flannery said.

That trouble becomes imminent for humans, too, when a 30-40 tonne gray whale begins floating in the bay, as happened earlier this year. The Army Corp of Engineers towed a body to a secluded beach for George and her team to perform a necropsy.

But in an unusual turn of events, George said her team hadn't yet made it to the first whale when they received a call about a second that needed immediate attention.

"Unfortunately, we had no place to put the whale, so it floated out of the bay," she said.

The bay area waters are somewhat closed off and relatively crowded with major container ships, ferries and public marinas, increasing the possibility of a whale - dead or alive - colliding with a vessel.

There's urgency "to get these whales out of traffic lanes as as quickly as possible", said Gary Reed, the director of vessel traffic for the US Coast Guard in San Francisco, who works with George and a coalition of industries to keep the harbour safe for whales and other wildlife.

The Coast Guard and ferry companies have implemented safety measures and captains are being trained to give the whales space, slow down and call in sightings. Reed hopes to soon install an infrared camera on the bay's Angel Island to monitor whales surfacing at night and in high traffic areas.

"Anything we can throw against the wall and see what sticks, we're willing to give it a try," he said.

Gray whales have mounted an incredible comeback before, notably when the US ended commercial whaling and introduced the Marine Mammal Protection Act in the early 1970s, said Michelle Barbieri Lino, a wildlife veterinarian with Washington state's SeaDoc Society. She was not part of the study.

"They are a species who can give us sense of awe of how these animals can recover from stressors and impact," she said, noting that grey whales are smart creatures that are probably experimenting with the bay as "a place to get a snack" on their long journey back to the Arctic.

This, she said, offers a glimmer of hope.

"If they have the protections they need in San Francisco Bay, this could be a place where they can successfully create a new foraging stopover to help them complete their migration and come back again and thrive," Lino said.