Ferries, cargo ships and tankers move through choppy waters in San Francisco Bay as whale activity increases during the same period mariners rely on predictable navigation, but until recently whales could go unnoticed. This week, researchers and operators launched an AI-powered whale-detection network designed to track gray whales day and night and to push alerts to vessels navigating the bay.
The system, called WhaleSpotter, uses artificial intelligence to scan the bay around the clock for whale blows and heat signatures up to 2 nautical miles away. When detections are made, the alerts are designed to be relayed to mariners with enough lead time to slow down or reroute, according to the project team.
Thomas Hall, director of operations for San Francisco Bay Ferry, said the approach is meant to give operators time to respond: “They’ll be able to make adjustments way before they get anywhere close.” Hall said the system would also produce data over time that could help operators understand where whales are “camping out,” allowing routes during whale season to be adjusted to avoid those areas.
The effort is taking shape as deaths of gray whales in the Bay Area have increased. The Marine Mammal Center found 21 dead gray whales in the wider Bay Area last year, which it described as the highest number in 25 years, and reported that at least 40% of those deaths were linked to ship strikes. At least 10 more have died in the Bay Area so far this year, and scientists said the true toll may be higher because some carcasses sink or are swept back out to sea before they are found.
Researchers say gray whales are also lingering inside a busy part of the estuary rather than passing offshore. Gray whales migrate along the California coast on a roughly 12,000-mile journey between breeding lagoons in Mexico and feeding grounds in the Arctic, but increasing numbers have been diverting into San Francisco Bay and staying for days or even weeks, a shift scientists increasingly link to climate change.
Rachel Rhodes, a project scientist at the Benioff Ocean Science Laboratory who led the initiative, described the navigation challenge that comes with that overlap. She said the concentration of animals in a corridor between Angel Island, Alcatraz and Treasure Island puts gray whales directly in the path of ferry routes and shipping lanes, adding: “It’s the worst place possible in terms of all the ship traffic,” and she said response teams have run out of locations to land dead whales.
Operationally, WhaleSpotter is built on a detection-and-verification workflow. Artificial intelligence flags potential whale sightings, and trained marine mammal observers verify those signals before alerts are sent via radio to ferry operators and vessel traffic controllers and posted publicly on the Whale Safe website.
The team said thermal cameras provide an advantage because they can operate overnight and in fog, when human observers may miss whale blows. One camera has been installed on Angel Island, and a second is expected to be fixed aboard a ferry traveling between downtown San Francisco and Vallejo to create what Rhodes described as a “moving data collection platform,” with additional cameras envisioned for the Golden Gate Bridge and Alcatraz to expand coverage across the bay.
The project also drew immediate reactions during early testing, with researchers describing a rapid surge in detections. Douglas McCauley, director of the Benioff lab, said: “Suddenly to have a full sense of how much whale activity is in this space honestly put me a little bit on edge,” while adding that the team planned to use the information to manage the area more effectively.
While the WhaleSpotter network targets gray whales and ship strikes, researchers also warned that a marine heat wave off the California coast is reshaping conditions that can raise risk for humpback whales. The heat wave is shrinking the band of cold, nutrient-rich water that supports prey such as krill, anchovies and sardines, and researchers said humpbacks are increasingly following that prey closer to shore, where the Dungeness crab fishery operates.
Kathi George, director of cetacean conservation biology at The Marine Mammal Center, said humpbacks can become entangled because of their behavior around fishing gear, saying: “Humpbacks are curious and they’ll scratch their backs on the gear.” She said that if a whale gets a line caught on its body, it may breach and roll, potentially leading to entanglement.
Regulators have closed parts of the fishery to conventional gear, a measure described as increasingly common in recent years as warming waters have increased overlap between whales and crab-fishing seasons. Thirty-six whales were confirmed entangled off the West Coast in 2024—described as the highest number since 2018—according to the National Oceanic and Atmospheric Administration, though scientists cautioned that many entanglements go undocumented.
California also approved commercial use of ropeless pop-up crab fishing gear this spring, a change designed to let fishermen continue through the season while reducing entanglement risk. Instead of floating surface buoys tethered to traps, the technology stores ropes and buoys on the seafloor until fishermen return and trigger an acoustic release that brings the gear to the surface, and supporters said the approach can keep harvesting going while dramatically reducing risk to whales.
As climate change continues to alter ocean conditions and whale movement, researchers said the overlap between whales, ships and fishing gear could persist. Caitlynn Birch, Oceana’s Pacific campaign manager and a marine scientist, said: “We will have to continue to be adaptive and science driven in terms of our management to reduce wildlife risk and keep fishermen on the water,” and added that California’s progress on whale-safe fishing technologies can guide other fisheries along the West Coast and nationally.