A growing number of bald eagles are soaring the skies of West Marin, proof that fierce protection can save a species that once perched on the brink of extinction. Other birds are paying a price for the eagle’s success: Surveys show that once-dense colonies of osprey, herons and egrets are scattering, as birds seek safety from harassment and predation by eagles. Still, the predators bring balance that naturalists say is a boon for ecosystems.

“Eagles are a great success story,” said Dave Press, a wildlife ecologist in the Point Reyes National Seashore. “But there are impacts associated with that.”

Long endangered, eagles have established at least three huge nests in the region—on the Inverness Ridge, at Kent Lake and perhaps at Walker Creek, according to Jules Evens, author of “The Natural History of the Point Reyes Peninsula.” Several youngsters that haven’t yet settled down have also been spotted.

Easily identified by their size and grandeur, the birds are most often seen over the waters of Drakes and Limantour estuaries. But they can also be seen swooping over Tomales Bay and perched in the tall Douglas firs above Inverness.

According to Mr. Evens, they likely all descended from a single pair that settled at Kent Lake in 2008. Kent Lake isn’t traditional eagle territory; the reservoir was created in 1958 by drowning forests in a valley south of Lagunitas. But the nest marked the return of eagles to Marin County after more than a century. 

The pair likely discovered Marin while migrating from northern California, said Inverness naturalist David Wimpfheimer. Every year, they produce two chicks. Over time, “that’s a lot of birds,” Mr. Evans added. 

Similar success stories are reported around the Bay Area. In 2019, there were six nests in Alameda County, five in Napa County and two in Sonoma County, according to Carie Battistone, the raptor coordinator at the California Department of Fish and Wildlife. 

Elsewhere in Marin, eagles are most commonly seen in Tiburon, but they’ve also been spotted above Corte Madera Creek and Novato’s Hamilton Wetlands, said Barbara Salzman of the Marin Audubon Society.

Eagles are especially abundant in the South Bay, where they have been spotted soaring over Stanford’s Inner Quad and San Jose’s Westfield Oakridge shopping mall. One pair has built a nest over a busy Milpitas elementary school.

During last autumn’s raptor migration over the Marin Headlands, volunteers counted five times the average rate of eagles: 0.11 eagles per hour, compared to an average of 0.02 eagles per hour. Despite the pandemic year’s truncated effort, volunteers counted 18 bald eagles, the highest number since annual monitoring started in 1986.

With sparse records before the turn of the last century, there is little understanding of eagles’ historical abundance in the area. Their bones have been identified in the Native American shell middens along the bay in Alameda County, according to David Shuford’s “Marin County Breeding Bird Atlas.” Before their recent comeback, one of the last confirmed nest sightings in the North Bay was in 1904, in Guerneville.

Eagles and other raptors were shot and poisoned by West Marin’s early ranchers and dairymen, who sought to protect their livestock. The pesticide D.D.T., which thinned and crushed eggshells, reduced numbers nationwide.

“Raptors were just persecuted endlessly,” Mr. Evans said.

By the mid-1960s, fewer than 30 nesting pairs of bald eagles remained in California—and they all lived up north. But the Endangered Species Preservation Act of 1966 helped reverse their fate, imposing penalties for shooting the birds. Use of D.D.T. was banned in 1972.

Eagles have also been aided by the creation of reservoirs such as Kent Lake.

Yet there, as elsewhere, eagles’ population expansion is impacting other bird populations.

“Bald eagles are scavengers and thieves, stealing food from other birds,” said Nils Warnock, the interim executive director of Audubon Canyon Ranch.

Osprey populations have plummeted at Kent Lake. Once home to 40 to 50 nests, it now has only about 10. 

Ospreys also seem to be declining along Inverness Ridge. “The bald eagles come in and they’ll just snatch the osprey chicks right out of the nest,” Mr. Press said.

Many ospreys have fled east, where they’re thriving. The number of osprey nests around San Francisco Bay jumped from 20 to 50 between 2012 and 2018, according to the Golden Gate Audubon Society. Along the Richmond shoreline alone, there are now 20 active osprey nests.

A similar drama took place at the Martin Griffin Preserve in Stinson Beach, where eagles and other predators have terrorized a rookery of herons and egrets that once hosted as many as 175 breeding pairs. 

Now the preserve is nearly empty. Starting in 2013, the nesting sites were largely abandoned, Mr. Warnock said. Although no one knows the exact cause, biologists suspect predators. When eagles fly overhead, they flush birds from their nests, allowing hungry crows and gulls to move in, though eagles also eat eggs. 

Some scattering herons and egrets probably flew over the Bolinas Lagoon to the Little Mesa, Mr. Warnock said. Others may have gone to the south end of Tomales Bay or the Point Reyes mesa, Mr. Wimpfheimer added.

After being gone so long, does the eagle still belong here?

“It’s generally better to have a good number of predators keeping things in balance,” Mr. Wimpfheimer said, adding, “But there is some negative impact. It remains to be seen how major that impact is. Talk to me in 20 years, if there are eagles all over the place.”