Researcher RJ Hawkins said the river otter discovery came after a camera near the Bronx River captured the surprising image.
Due to extreme flooding, the water in the enclosure rose high enough that a sea lions swam out of their exhibit.
Jim Breheny, Director of the Bronx Zoo, said a female sea lion was able to swim out of her pool due to flooding of the plaza caused by the heavy rain.
The wayward bird had been perched in the tree since before 8 p.m. Wednesday night, after flying off zoo grounds.
A crowd gathered around the peacock perched at E.180th Street and Vyse Avenue.
Radiographs showed that the alligator had ingested a bathtub stopper about 4 inches wide.