JFK International Airport was already redirecting flights to the nearby Newark.
Flights were currently delayed up to 90 minutes at JFK, but Newark is reporting two-hour delays.
New York’s LaGuardia Airport is also experiencing delays of an hour and a half, and travellers in Philadelphia have to wait on average 58 minutes, reports the Federal Aviation Administration.
Areas spanning from New England to the Midwest can expect three to five inches of rain.
New York City was hit by a freak storm two weeks ago which brought flash floods and booming thunderstorms.
Subway stations were shut down as water submerged tracks leaving many commuters stranded.
Meanwhile, additional showers, periods of heavy rain, and thunderstorms will continue along and ahead of the associated cold front as it extends southwest from the low through the Southern Plains with waves of low pressure.
There is a moderate risk of severe thunderstorm development from Ohio through the Lower Northeast, while areas from the Upper Great Lakes and the Mid-Mississippi Valley northeastward to southern New England are at slight risk for severe weather development.