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The captain of the boat that capsized in off Liberty Island in New York Harbor late Saturday — killing a mother and her infant daughter — was hit with more than a dozen charges for driving it dangerously overloaded, sources said.

Manuel Hernandez, 46, was slapped with 13 charges of reckless endangerment after the 22-foot motorboat he was operating flipped over just before 10:30 p.m. Saturday, with more raps pending, law-enforcement sources said Sunday.

The vessel, a bowrider with front seating, was overloaded with 14 people on board, NYPD sources told The Post. Online sites say its capacity is typically 10 to 12.

Two passengers from College Point, Queens, died: 27-year-old Sara Sanchez and her 5-month-old daughter Antonella Garcia.

Sanchez’s boyfriend, who was the baby’s father, also was on board the boat at the time of the tragedy, according to sources.

Multiple agencies, including the NYPD, the FDNY, the US Coast Guard and Air Sea Rescue, scrambled to the scene, where Hernandez, whose last known address was a swanky Midtown Manhattan condo building, was taken into custody.

Pictures and video on Sunday morning show the upturned vessel being lifted out of the water.

Video of Saturday night’s incident shows blue and red emergency craft lights in the dark harbor searching the waters after the vessel capsized.

NYPD helicopters could be seen hovering overhead while FDNY vessels patrolled the waters to save survivors.

The remaining 11 passengers were removed from the water and transported to Brooklyn’s Lutheran Hospital in stable condition with minor injuries.

This is a developing story. Please check back for updates.

“No! Why? Why? No!” a loved one of one of the victims wailed at the hospital on Saturday night.

This is a developing story. Please check back for updates.

Some of the survivors could be seen still clutching their life jackets in the hospital lobby.