Gray whales are using San Francisco Bay as a temporary refuge to survive, but for many, it's becoming a fatal endpoint. As climate change reshapes ocean ecosystems, these marine mammals, known for their long-distance migrations, are beginning to exhibit unusual behavior, with some individuals being spotted foraging in the busy and dangerous waters of San Francisco Bay, a choice that often ends in tragedy.
Gray whales typically migrate long distances between their Arctic feeding grounds and the warm breeding lagoons of Baja California, Mexico. However, climate change is disrupting their food supply in the Arctic, making these ocean giants even more vulnerable. Gray whale populations have declined by more than 50% since 2016, according to the National Oceanic and Atmospheric Administration, and sightings of young whales have become rare.
San Francisco Bay has not historically been part of the gray whale migration route. That began to change in 2018, when gray whales began to appear more frequently in the waters, accompanied by a troubling increase in deaths. Researchers launched an in-depth investigation to understand what was happening to these so-called "Gulf gray whales" and whether they would return year after year.
"When gray whales surface, they have a relatively low profile, which makes them difficult to spot in conditions such as fog common in San Francisco Bay," a team led by Sonoma State University's Josephine Slathaug explains in an article published in the journal Frontiers in Marine Science. "In addition, San Francisco Bay is a heavily trafficked waterway, with the Golden Gate Strait acting as a bottleneck through which all ships and gray whales must enter and exit."
To conduct the survey, scientists created a catalog of individual gray whales using records and photos of opportunistic sightings collected by the public between 2018 and 2023, as well as more systematic surveys conducted between 2023 and 2025. They compared these records with necropsy data from stranded gray whales. Identification efforts rely on unique markings on each gray whale's skin, although these fade quickly after death, meaning some individuals may not be matched.
Research results show that a total of 114 individual gray whales were recorded in San Francisco Bay between 2018 and 2025. Only four gray whales have been observed in more than one year, suggesting that most gray whales do not return. Researchers believe the bay may have served as an emergency feeding station for gray whales in poor condition, as very emaciated gray whales have been observed feeding in other unusual habitats.
Despite possible use of the bay as a temporary refuge, many gray whales do not survive. From 2018 to 2025, a total of 70 gray whales were found dead in the area. Thirty of them were hit by boats, while many other individuals with known causes of death showed signs of malnutrition. Of the 45 potentially identified dead gray whales, 21 matched cataloged individuals.
Co-author Becca Lane of the Center for Coastal Research noted: "At least 18 percent of individuals identified in San Francisco Bay later died in the area. Our broader analysis of local strandings in and outside San Francisco Bay found that more than 40 percent of these gray whales died from vessel-induced trauma."
In 2025, 36 gray whales entered the bay alone, sometimes in groups of more than 10. Researchers say more work is needed to understand how gray whales use the bay and how to reduce the risks they face. Further surveys and necropsies could help determine whether the lower numbers of returning gray whales are due to high mortality rates, and whether deaths are primarily caused by starvation, boat strikes or a combination of the two. Weakened gray whales may have a harder time avoiding ships.
Efforts to reduce these risks may include education programs for commercial vessel operators or changes to ferry routes. "In San Francisco Bay, the greatest threat to these gray whales is vessel traffic," Lane said. "Continuous monitoring will help illuminate their distribution patterns and behavior within the bay, which may affect risk. Route changes and speed limits have been found to significantly reduce the lethal effects of vessel strikes on large cetaceans, and risk assessments can help determine the most effective strategies to protect these animals."
Scientists warn that important gaps remain in understanding how individual gray shad move and behave at day-to-day scales. Even so, the findings provide valuable insights into how gray whales respond to rapidly changing environmental conditions.
"This study is our best analysis of the data collected, but it's important to consider that we don't have a complete picture of each gray whale's movements on a daily time scale," Slathaug said. "These results are an important piece of the larger puzzle of what's happening as the entire population is trying to adapt to climate change in real time."