The birds had been spotted in Southold creeks in recent days.
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Area residents joined hands and kayaks to form a human chain to protect the swans until rescuers arrived.
It's believed the swans were abandoned by someone who owned them.
Officials say they are unable to defend themselves in the wild because they have been domesticated.
Once they were captured, both swans were calm as they were taken away.
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The group Long Island Orchestrating for Nature said they will take care of the birds until they find an appropriate home.
The group says it has already received several offers.
MORE NEWS: Seagull hits teen in face while on Jersey Shore ride
Seagull hits teen in face while on Jersey Shore ride
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