The discovery was made at the water pollution control plant on Ryawa Avenue in Hunts Point.
Workers spotted the possible human remain, described as a leg from the knee down, with the foot attached, on a conveyor belt as recycled materials passed them just before 9 a.m.
They stopped the conveyor belt and looked for additional remains, but none were found.
Police fear it could belong to a child, even possibly a newborn.
"It's unbelievable," said Efraim Basom, who works across the street at a seafood warehouse. "It's starting to be scary in this area."
It remains unclear if it was dumped at the location or came from the water and got caught in the system.
The medical examiner was to make the determination if it is a human body part.
The plant is an initial filter point for all of the Bronx, so the possible remains could have come from anywhere in the borough.
The investigation is ongoing and detectives are waiting for more information from the medical examiner.
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