That's because the iconic birds, which were wiped out on the islands in the 1960s, have returned to find that their traditional food sources have been greatly reduced.
To make ends meet, the predatory birds may be forced to scavenge on marine mammal carcasses, the blubber of which is still laced with DDT—the same pesticide that infamously led to the near extinction of bald eagles across the United States.
(Related: "Antarctic Melt Releasing DDT, Tainting Penguins.")
"Eagles are opportunistic, and as their population grows, they might switch their diets ... to include carrion from local sea lion colonies, which is a very abundant food source, for sure," said study co-author Seth Newsome, a biochemist at the Carnegie Institution for Science in Washington D.C.
The northern Channel Islands are home to some of the largest seal and sea lion rookeries in the United States, with populations in the tens and hundreds of thousands, Newsome added.
What's more, some conservationists fear that a bald eagle boom will lead to declines in some of the Channel Islands' other rare species, such as the island gray fox. (See a Channel Islands fox picture.)
Tracing Bald Eagles' Historic Diets
Currently about 70 adult bald eagles and roughly a dozen chicks live across all eight of the Channel Islands, thanks to several reintroduction programs.
(Related: "Bald Eagles Soar Off Endangered Species List, But Will Act Be Weakened?")
To find out how the reintroduced birds might affect the modern ecosystem, Newsome and colleagues analyzed the remains of prey species left in historic and prehistoric nests on the Channel Islands. Based on that data, the scientists reconstructed the bald eagle's regional diet from about 25,000 years ago to the present.
The team found that populations of seabird species the eagles had historically preyed on, such as Brandt's cormorant and Cassin's auklet, are now greatly reduced on the islands.
Overfishing in the Channel Islands region may also be depriving the eagles of fish they would otherwise target as prey, the study says.
Because bald eagles will hunt, scavenge, or steal their food, the scientists think the birds will turn to any prey they can find on today's islands—including the bodies of marine mammals, many of which are of pups that never make it to adulthood.
Eagles feeding on tainted sea mammals definitely creates a worry for scientists, said Peter Sharpe, a wildlife biologist at the Institute for Wildlife Studies in Avalon, California, who was not involved in the new study.
"There is a concern," Sharpe said. "We know that [the eagles] have always fed on dead marine animals. DDT and other contaminants are often stored in the blubber, which is most accessible to anything feeding on them."
DDT was banned in the 1970s, in part because it had been found to be weakening bird eggs, resulting in serious population declines. But the chemical lingers in the sediments and waters of the Channel Islands environment, Sharpe said.
(Related: "DDT to Return as Weapon Against Malaria?")
Eagles Unlikely to Want Their Food Rare
Besides monitoring the eagles carefully, there is little scientists can do to protect the birds, Sharpe added.
The DDT, he said, "just has to eventually work its way out of the ecosystem."
Study author Newsome and his team also worry the Channel Island bald eagles could threaten native seabirds, such as the Xantus's murrelet, and small mammals, such as the island fox—which are perilously close to extinction themselves, the team notes. (See pictures of some of the rarest species in the U.S.)
But Sharpe thinks such a scenario is unlikely: "Bald eagles tend to feed on what's most prevalent in the environment," he said. "So it's unlikely they're going to feed on any rare species."
The bald eagle research was published online this week in the Proceedings of the National Academy of Sciences.