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An archipelago of sorts, a collection of rock formations dotted with scrub brush, has been home to New York's mental institutions, quarantine hospitals and some of the city's most famous residents. Long abandoned by people, some of the islands have now become home to migratory birds that have flocked there in numbers not seen in decades.

The Audubon Society of New York, in partnership with New York Water Taxi, took visitors on a tour of the islands yesterday to showcase the bustling wildlife on display just a short boat ride away from asphalt, concrete and steel towers of Manhattan. Cormorants, egrets, herons and American oystercatchers are just some of the species not usually spotted in New York that have congregated on the islands, which include North and South Brother Islands, between Rikers Island and the Bronx, and Mill Rock, just north of Gracie Mansion.

The tour passes the mouth of Newtown Creek, a gritty industrial area along the Brooklyn-Queens border where the Rockefellers built their first Standard Oil refineries in the late 19th century and where an oil spill in 1950 larger than the Exxon Valdez disaster polluted the soil and waterways in Greenpoint. For the past two decades the Audubon Society has been working to help clean the waters around New York and bring birds back to the area.

That effort has been so successful that the organization now operates scheduled boat tours for close-up views of wild birds that have become hugely popular with birdwatchers. Yesterday's trip, from South Street Seaport, was a preview. The summer tours begin tomorrow.

''Look! Oystercatchers,'' said Gabriel Willow, a tour guide who works as a teacher and naturalist at the Audubon Center in Prospect Park, almost breathless as he interrupted his story about the history of South Brother Island, where Babe Ruth used to practice his batting, to point out the small birds flying just above the tree line. ''There's three of them. It's an oystercatcher orgy!''

The birds, related to sandpipers, are brown and black with red beaks, and, Mr. Willow said their presence is a sign that the local waterways are cleaner.

''If there are oystercatchers, there's probably oysters, and if there are oysters, water quality is improving,'' he said.

More than a dozen species of water birds have returned to the area since the 1970's. There are about eight species of heron and egret alone.

Mill Rock Island, home to 50 pairs of black-crowned night heron, in the most dangerous part of the channel because of its swift waters and eddies, was the site of the largest planned explosion before testing began for the atomic bomb.

In the 1700's and 1800's, thousands of ships ran aground in the channel because of rocks, shoals and reefs near Mill Rock. One island, known as Flood Rock, was a particular problem, so New York decided to get rid of it, as well as several other hazards. Workers drilled holes in the shoals and rock near Mill Island and on Flood Island in 1885, and set off an explosion that was felt in New Jersey and sent a geyser of water and debris 250 feet into the air.

It obliterated Flood Island, and pieces of rock were used as fill to bring two small islands together to form what is now Mill Rock.

North Brother Island, where egret and heron nests are concentrated, was home to Mary Mallon, better known as Typhoid Mary, from 1907 to 1938. After World War II, the military built homes there for returning veterans.

One of those veterans wrote a short story that was turned into the screenplay for the classic Hitchcock film, ''The Birds.''

''He apparently was freaked out about the birds on the island,'' Mr. Willow said. ''Now we have a whole new appreciation for the birds.''

Photo: Egrets on South Brother Island in the East River have grown in numbers, as have other birds on two other islands near Rikers Island. (Photo by Richard Lee for The New York Times)

Map of Manhattan, Bronx, and Queens highlighting North Brother Island, South Brother Island, and Mill Rock Park: Some migratory birds are flocking to three islands in the East River.