Hoboken and parts of Brooklyn and the Bronx were hit especially hard, with cars submerged and ruined and water lapping up to the doorsteps of some schools.
The flood waters rose rapidly on Route 1 & 9, where drivers tried to make their way through unaware that the water would come over the front of the car.
The roadway was shut down in one direction as the water slowly receded. Several people had to be rescued from their vehicles, while others made daring escapes as the murky water was rushing in.
Flooding also trapped several vehicles at the Jersey City-Hoboken border, right underneath the New Jersey Transit railroad bridge.
Those living in the area have been forced to park on the street because Superstorm Sandy destroyed the garage on the lower level of their building.
Conditions were not expected to be as bad Thursday, but no one anticipated the amount of water that arose Wednesday, either.
That is keeping residents on edge as potentially heavy storms move through.