Gray whales are known for their long migrations between the food-rich Arctic Ocean and the warm lagoons of Baja Mexico. However, as ocean conditions change due to climate change, some whales are behaving in unexpected ways. In recent years, many gray whales have been seen feeding in unfamiliar areas, such as the busy waters of San Francisco Bay. Researchers studying the unusually high number of whale deaths found that nearly 20% of gray whales seen entering the bay did not survive, and many died in boat strikes.
“Gray whales maintain a low profile when surfacing, which makes them difficult to see in the foggy conditions common in San Francisco Bay,” said lead author Josephine Slatthaug of Sonoma State University. Frontiers of marine science. “Additionally, San Francisco Bay is a busy waterway, and the Golden Gate Strait is the bottleneck for all traffic and whales to enter and exit.”
Climate change and changes in whale behavior
Gray whales typically do not feed during migration to their tropical breeding grounds. Instead, they rely heavily on the food they consume in arctic feeding grounds. But warming temperatures are destroying these food sources, putting whales at increased risk. According to the National Oceanic and Atmospheric Administration, the population has declined by more than half since 2016, and sightings of calves are becoming rarer.
San Francisco Bay has not historically been part of the gray whale migration route. The situation began to change in 2018, when whales began to appear more frequently and local fatalities also increased. Scientists have begun an effort to better understand these “bay greys” and determine whether they are repeat visitors or just one-time visitors.
Tracking gray whales in San Francisco Bay
To study, the researchers cataloged individual whales using opportunistic sightings and photos submitted by the public from 2018 to 2023, as well as more structured surveys conducted from 2023 to 2025. They compared these records with necropsy data from stranded whales. Identification relied on unique markings on each whale’s skin, but these markings can disappear after death, meaning some matches may have been missed.
A total of 114 whales were recorded in the bay during the study period. Only four whales have been observed for more than a year, suggesting that most do not return. Scientists believe the bay may be acting as an emergency feeding site for whales in poor condition, as unusually thin individuals have been observed foraging in other non-traditional habitats.
High mortality rates from ship collisions and starvation
Despite using the bay as a potential feeding ground, many whales do not survive. Between 2018 and 2025, 70 gray whales were found dead in the surrounding area. It was confirmed that 30 of these vessels were involved in collisions with ships. Of the remaining whales whose cause of death could be determined, many showed signs of malnutrition. Researchers were able to match 21 of the 45 identifiable dead whales to individuals in the catalog.
“At least 18% of the individuals identified in San Francisco Bay later died in the area,” said co-author Bekah Lane of the Coastal Research Center. “Extensive analysis of local strandings in and around San Francisco Bay found that more than 40 percent of these whales died from vessel trauma.”
Protection measures are urgently needed
Scientists emphasize the need for further research to better understand how and why whales use the bay. In 2025 alone, 36 whales entered the area, sometimes in pods of more than 10. More detailed tracking and additional necropsies could help determine whether the low number of whales returning is due to high mortality rates, or whether the main cause of death is starvation, ship strikes, or both. A weakened whale may be unable to avoid an oncoming ship.
Preventive measures could include educating commercial vessel operators, adjusting ferry routes and enforcing speed limits in high-risk areas.
“In San Francisco Bay, the biggest threat to these whales is ship traffic,” Lane said. “Continued monitoring will help uncover whale distribution patterns and behavior within the bay that may impact risk. Route changes and speed limits have been found to significantly reduce vessel strike mortality for large whales, and risk assessments will help identify the most effective strategies to protect these animals.”
Citizens under pressure
Researchers warn that there are still gaps in our understanding of whales’ daily movements and behaviors. But the discovery provides an important snapshot of how gray whales are responding to rapidly changing environmental conditions.
“While this study is the best analysis of the data we have collected, it is important to consider that we do not have a complete picture of each whale’s movement on a daily timescale,” Slathaug said. “These results are an important piece of the larger puzzle of what’s happening across populations as we try to adapt to climate change in real time.”
