Gray whales are known for their long migration between food-rich Arctic waters and the warm lagoons of Baja Mexico. But as climate change alters ocean conditions, some whales are behaving in unexpected ways. In recent years, a number of gray whales have been spotted feeding in unfamiliar areas, including the heavily trafficked waters of San Francisco Bay. Researchers studying an unusually high number of whale deaths have found that nearly 20% of the gray whales seen entering the Bay did not survive, with many killed by boat strikes.
“Gray whales have a low profile to the water when they surface, and this makes them difficult to see in conditions like fog which are common to San Francisco Bay,” explained Josephine Slaathaug of Sonoma State University, lead author of the article in Frontiers in Marine Science. “Additionally, San Francisco Bay is a highly trafficked waterway, and the Golden Gate Strait serves as a bottleneck through which all traffic and whales must enter and exit.”
Climate Change and Shifting Whale Behavior
Gray whales typically do not feed during their migration to and from tropical breeding grounds. Instead, they rely heavily on the food they consume in Arctic feeding areas. However, warming conditions are disrupting those food sources, leaving whales increasingly at risk. According to the National Oceanic and Atmospheric Administration, the population has declined by more than half since 2016, and sightings of calves have become rare.
San Francisco Bay was not historically part of the gray whale migration route. That began to change in 2018, when whales started appearing there more frequently, along with a rise in local deaths. Scientists launched an effort to better understand these “Bay Grays” and determine whether they were returning visitors or one-time arrivals.
Tracking Gray Whales in San Francisco Bay
To investigate, researchers built a catalog of individual whales using opportunistic sightings and photographs contributed by the public between 2018 and 2023, along with 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, though these markings can fade after death, meaning some matches may have been missed.
In total, 114 individual whales were documented in the Bay during the study period. Only four were observed in more than one year, suggesting that most whales do not return. Scientists believe the Bay may act as an emergency feeding stop for whales in poor condition, as unusually thin individuals have been observed foraging in other nontraditional habitats as well.
High Mortality From Ship Strikes and Starvation
Despite using the Bay as a potential feeding refuge, many whales do not survive. Between 2018 and 2025, 70 gray whales were found dead in the surrounding region. Of those, 30 were confirmed to have been struck by vessels. Among the remaining whales where a cause of death could be determined, many showed signs of malnutrition. Researchers were able to match 21 of 45 identifiable dead whales to individuals in their catalog.
“At least 18% of the individuals identified in San Francisco Bay later died in the area,” said Bekah Lane of the Center for Coastal Studies, co-author. “Our broader analysis of local strandings both inside and outside San Francisco Bay found that over 40% of these whales died of trauma from vessels.”
Urgent Need for Protection Measures
Scientists emphasize the need for more research to better understand how and why whales are using the Bay. In 2025 alone, 36 whales entered the area, with groups sometimes exceeding 10 individuals. More detailed tracking and additional necropsies could help determine whether the low number of returning whales is due to high mortality rates, and whether deaths are primarily caused by starvation, vessel strikes, or a combination of both. It is possible that weakened whales are less able to avoid oncoming ships.
Preventive steps could include educating commercial vessel operators, adjusting ferry routes, or implementing speed restrictions in high-risk areas.
“In San Francisco Bay, the biggest threat to these whales is vessel traffic,” said Lane. “Continued monitoring will help illuminate their distribution patterns and behaviors while within the Bay, which can impact risk. Route changes and speed restrictions have been found to significantly reduce vessel strike mortality to large whales, and an assessment of risk can help identify the most effective strategies to protect these animals.”
A Population Under Pressure
Researchers caution that there are still gaps in understanding whale movements and behavior on a day-to-day basis. However, the findings provide an important snapshot of how gray whales are responding to rapidly changing environmental conditions.
“This study is our best analysis of the data we collected, but it’s important to consider that we do not have the full picture of each whale’s movements on a daily timescale,” said Slaathaug. “These results are an important piece of the larger puzzle of what is going on in the overall population as they attempt to adapt to climate change in real time.”