The captain of the boat that capsized in New York Harbor late Saturday — killing a baby and a 27-year-old woman — was hit with more than a dozen charges for driving it while dangerously overloaded, according to sources.

The operator, a 46-year-old Manhattan resident who has not been publicly identified, faces 13 charges of reckless endangerment after the motorboat he was steering flipped over off the coast of Liberty Island just before 10:30 p.m. Saturday, with more charges pending, according to sources.

The vessel, a 22-foot bowrider motorboat, was overloaded with 14 people on board, NYPD sources told The Post.

Two passengers are confirmed to have died, including a 5-month-old baby and a 27-year-old woman from Queens. Neither has been identified pending family notification, the NYPD said.

Multiple agencies, including the NYPD, the FDNY, the US Coast Guard and Air Sea Rescue, were scrambled to the scene and the captain of the vessel was taken into custody.

Video of the 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.

“No. Why? Why? No,” a loved one of one of the victims could be heard yelling in horror at the hospital on Saturday night.

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

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

SOURCE: NYSPOST.COM