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pring and fall can be magical times along California’s coast. Gazing out to sea, you might glimpse a spout of seawater or a glistening fin slice through the waves — whales! It’s thrilling to spot these massive mammals as they migrate from Alaska to Mexico in the fall and back north in the spring. But gray whales, in particular, have been washing up dead on Bay Area beaches at alarming rates over the past several years.

Five-year-old Caleb Whan is very interested in whales. He asked Bay Curious a bevy of questions about what they eat and where they live, which is how he ends up trudging across a windy Sausalito beach with a veterinary pathologist, his dad and me. We soon reach the large, smelly marine mammal carcass.

“Hey, that whale looks so funny,” says Caleb. The whale carcass has decomposed so much that it’s difficult for us to identify its parts, but the Marine Mammal Center’s Pádraig Duignan points out where the gray whale’s bones are broken.

Gray whales can sometimes be spotted in San Francisco Bay, though Duignan says this isn’t usually one of their stops along their long migration route.

“But last year, or last season, several did [enter the bay],” he says. “They were looking for food.”

“What do they eat?” Caleb asks.

“They will eat these guys,” Duignan says, pointing to tiny oysters in his hand as he lets sand filter through his fingers. “Shellfish and little shrimp, all sorts of little creatures that live on the bottom.”

Looking at the damaged body, Caleb has another question: “What happened to this whale?”

“Unfortunately, it was hit by a ship and the ship broke some of its bones,” Duignan says, adding the animal likely died at sea and only washed ashore some days later. When it did, Duignan and his colleagues performed a necropsy — that’s an animal autopsy — as they do whenever whales or other dead marine mammals wash ashore in the area.

“We collect a lot of samples, run a lot of laboratory tests,” he says. “This one was convenient for us in that it was literally right beside our center, but often we have to travel to where they are.”

The Marine Mammal Center is just half a mile up the hill from Rodeo Beach and responds to whale deaths from Pacifica to Point Reyes, with occasional trips as far north as Mendocino County and as far south as San Luis Obispo. Whales that die within San Francisco Bay are generally towed to Angel Island, where the necropsies are performed. In 2021, gray whale deaths occurred at Crissy Field and Ocean Beach in the city, Muir Beach and McClures Beach in Marin County, and the Fitzgerald Marine Reserve in San Mateo County, among other locations.

It’s easy to see the blunt trauma that killed the Rodeo Beach whale, but other animals present more of a mystery to Duignan and his colleagues. The recent uptick in whale deaths has even prompted an international investigation.

Nineteen gray whales have washed up on California’s coast this year, and in many cases there were no clear signs of what killed them. Communities all along the whales’ long migration route are noticing a similar trend, and whale deaths have been above normal for the past three years.

Duignan says about a third of the gray whales have been hit by ships. But that leaves a lot more fatalities unexplained.

“We’re not seeing any one particular cause of death in all of these whales that we see, some of them in San Francisco Bay, some of them outside the bay,” says Moe Flannery, senior collections manager for birds and mammals at the California Academy of Sciences. She’s also been looking into the spate of gray whale deaths, what the National Oceanic and Atmospheric Administration calls an “unusual mortality event.” In fact, scientists from Alaska to Mexico are working together to unravel the mystery.

When a dead whale is reported in the Bay Area, the necropsy team heads out to take photos, measurements and samples. Flannery’s group focuses on bones and muscle systems, while the folks from the Marine Mammal Center look at stomach contents and test for diseases.

“We are seeing some [whales] that are showing signs of malnutrition or emaciation,” Flannery says. “We are seeing some that are showing signs of trauma from, like, an orca predation. We are seeing some with signs of trauma from possibly a ship strike. And there are a lot of them that we just don’t know why they died.”

Crabbers team up with scientists

E

ven as the scientists puzzle out what’s going on, there is some good news.

Back in 2016, there was a spike in West Coast whale entanglements — 48 of the big animals got caught in fishing lines and gear, some of them fatally. Of those, 19 were traced to commercial Dungeness crab gear. So the state worked with fishermen to try to understand what was happening, and what they could all do to prevent the problem.

Dick Ogg is a commercial Dungeness crab fisherman who got involved with the state effort. On a clear morning, with the sun just rising, Ogg maneuvers his boat out of the harbor in Bodega Bay. He’s been fishing these waters for more than two decades, captaining his small boat with two hired workers. He says he often sees whales.

“I would say 99.9% of the time you’ll see whales at one point or another,” he says. He claims he can even smell a whale, noting that what comes out their blowholes can be rather pungent. But there are no breeches or other obvious whale sightings on this Saturday.

When the 2016 data implicating crabbers in whale deaths came out, he and others started taking a closer look at their setups. Ogg explains that the standard crab gear kit used to include lead weights that would cause the lines to form a W-shape in the water as the crab pots sank to the ocean floor.

“We began to think that that might be a potential place where interaction could occur,” he says. The looping line “could wrap around an animal.”

Ogg and other crabbers voluntarily switched to a system that allows the lines to run taught from the 100-pound crab pot to a buoy floating on the water’s surface.

If a whale hits that, he says, “it tends to want to roll off rather than whip around with the lead.” That means the whale is more likely to safely swim away rather than getting so tangled that it’s either injured or killed.

The switch seems to be helping. This year’s gray whale necropsies in California have not found any evidence implicating crab gear. However, the Dungeness fishery can still be subject to delays or closures if whales or other protected species are present.

Flannery, at the Cal Academy, says there are still many hypotheses about why the gray whales are dying. Maybe it’s climate change: Gray whales typically eat a year’s worth of nutrition in Alaska, but it’s possible the waters there have become too warm to support the food they need. Or, it could be a natural population cycle: Flannery says scientists saw a similar sudden increase in deaths about 20 years ago, also for about three years.

Overall 2021 has not been as bad as last year, and 2019 was the worst. The international network of pathologists and scientists continues to look for answers to gray whale deaths. For his part, Duignan thinks climate change is a likely suspect, because the warming planet already has changed arctic ecosystems dramatically.

“[A changing climate] could affect where they [whales] find their food, how much food is available to them and, in the long run, if they’ll be able to sustain their population,” he says.