Mayor Michael Bloomberg has ordered the evacuation of "Zone A," comprising the city's lowest-lying neighborhoods.
In Brooklyn, that includes parts of Red Hook, Coney Island and Manhattan Beach.
In Queens, Zone A encompasses part of Long Island City and the Rockaways.
City schools will be closed on Monday, according to Bloomberg. Alternate side parking rules will be suspended.
Transit officials will begin to wind down subway service at 7 p.m. Buses will run until 9 p.m.
65 city shelters are open throughout the city. For a map of locations, visit WNYC's website.
Bloomberg said the city's forecast storm surge had increased to as much as 6 to 11 feet above average tide. The danger for the city begins Sunday night and at the height of the storm on Monday night and Tuesday morning.