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Hundreds of flights were canceled or delayed at the three major airports serving New York City Sunday, giving travelers major headaches as rainstorms and deadly flooding pounded portions of the Northeast.

More than 1,600 flights were canceled across the country — with Newark Liberty International, John F. Kennedy International and LaGuardia airports experiencing the most delays and cancellations, according to FlightAware.

The New Jersey airport took the crown for the greatest number of flight cancellations of all US airports Sunday.

Newark had a combined 365 incoming and outgoing flights — about 30% of all its scheduled flights — canned and another 461 delayed, FlightAware data showed.

The air travel snafu wasn’t limited to actual plane operations, either.

One traveler coming from Chicago told The Post they were among dozens of passengers who waited for their baggage for more than two hours after landing in Newark.

The United customer said only about a third of passengers’ luggage arrived at the baggage claim and the rest seemed to be missing.

United Airlines didn’t immediately respond to an inquiry about the reportedly lost luggage.

Newark Airport had the greatest number of flight cancellations among US airports Sunday. Twitter / @Divanick
Regions across New York state saw between one and three inches total of rain on average. G.N.Miller/NYPost
Several areas throughout the Northeast had flash flood warnings. NWS

JFK Airport came in second for the greatest number of canceled flights after Newark — with a total of 331 cancellations both to and from the airport — and LaGuardia wasn’t far behind with 280 grounded flights, according to flight tracking data.

All three airports warned customers to check their flight status before arriving at the airport due to heavy rain and fog in the metro area.

Thunderstorms, severe rain and flash flooding affected much of the greater New York area Sunday.

Many Newark customers complained about delays and cancellations on Twitter. Twitter / @officialsanjivg

Stranded #ewr airport, delayed flight 2 hours, in a plane for 5 more. Deplaned at 1230 am. I can't even get a hotel. The line to rebook next flight almost 1/2 mile long. Now standing in cue for past 1-1/2 hour and it may take another 2. Good job #United pic.twitter.com/ol8POZNG8B

— Sanjiv Goyal (@officialsanjivg) July 15, 2023

The National Weather Service issued a flash flood warning for parts of Queens and the Bronx in the afternoon.

Most areas in New York saw between one and three inches of rain total — with some spots totaling as much as five inches by nightfall.

The wet weather came after the Empire State was slammed with torrential downpours last weekend.

The rain and subsequent flooding killed one New Yorker and caused about $50 million in damage, Gov. Kathy Hochul said.

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