The AccuWeather forecast says 1 to 2 inches of rain is possible, the heaviest rainfall occured from 2 to 7 p.m. The Jersey Shore could see the highest amounts.
The heavy rain, along with thawing ice, could lead to ice jams in area waterways.
There will also be strong wind gusts, with a wind advisory issued for New York City, Long Island and coastal Connecticut.
The flood watch is in effect until 6 a.m. Sunday for New York City, Long Island, Rockland and Westchester counties, and Bergen, Essex, Passaic, Union, Hudson, Hunterdon, Middlesex, Morris, Somerset, Sussex, Warren and western Monmouth counties in New Jersey.