Officials are looking into whether the boat was an illegal charter.
The operator of a boat that capsized in New York Harbor, leaving a mother and her baby daughter dead, is facing federal charges of negligence as a ship captain resulting in death and misconduct as a ship captain resulting in death, ABC New York station WABC reported.
Manuel Hernandez, 46, was taken into federal custody on Monday, according to a U.S. official. He appeared in court Monday afternoon and is set to be released on $50,000 bail, WABC reported.
Hernandez was initially arrested on state charges -- 13 counts of reckless endangerment -- according to the New York Police Department.
On Saturday night, the boat overturned near the Statue of Liberty, sending all 14 on board into the water, the Coast Guard said.
The NYPD identified the two people killed as 27-year-old Sara Sanchez and 5-month-old Antonella Garcia of Queens, New York. Sources told ABC News the victims were mother and daughter.
The 12 survivors were rescued with minor injuries, the Coast Guard said.
Sanchez leaves behind her husband, who was on the boat and survived, and their 6-year-old son, who was not on the boat, WABC reported.
Investigators are looking into whether the boat was an illegal charter operation, the Coast Guard said.
ABC News' Luke Barr contributed to this report.
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