Boat recovered by authorities after it capsized near the Statue of Liberty in New York Harbor (Source: Luiz C. Ribeiro)

Federal prosecutors have taken over the case against the captain of a boat that capsized in the busy waters near the Statue of Liberty on Saturday night, killing a young mother and her 5-month-old daughter, as authorities investigate what caused the boat to overturn.

Manuel Hernandez, 46, of Manhattan, was arrested early Sunday and charged with 13 counts of reckless endangerment, just hours after the boat carrying 14 people overturned in New York Harbor, the New York Police Department said.

He has since been transferred to federal custody after receiving treatment at a hospital, according to CNN affiliate WABC. It is not yet clear when Hernandez is scheduled to appear in court, or whether he has retained an attorney.

Authorities are investigating whether the captain was running an illegal charter without required credentials and safety equipment, the Coast Guard said. Investigators believe the boat was likely over capacity, a law enforcement source briefed on the matter told CNN.