Following the storm, which blasted NY on Thursday, passengers were kept on planes and waited hours to retrieve luggage as flights were delayed and canceled, and a backup to get to terminal gates built up.
The break happened in Terminal Four, which is a main worldwide hub for the airport serving mainly Delta Airlines.
Global arrivals at the terminal were suspended.
"These included frozen equipment breakdowns, difficulties in baggage handling, staff shortages, and heavier than typical passenger loads", the statement said. Flights later resumed but with delays, it said.
It was unclear what caused the break, which sent about 3 inches of water into the terminal's west end.More news: Largest known prime number discovered
JFK was one the parts of NY that saw record lows for January 7, including four degrees Fahrenheit (minus 15.5 degrees Celsius).
When operations resumed on Friday, the backlog led to hundreds more delays or cancellations, crowding the terminals with stranded passengers.
Extreme cold and ongoing recovery from Thursday's brutal winter storm that snarled air traffic to the airport "created a cascading series of issues for the airlines and terminal operators over the weekend", the Port Authority of NY and New Jersey, which manages the airport, said in a statement earlier Sunday.
The flooding hit just as the airport was crawling back to normal after a winter storm labeled a "bomb cyclone" forced the airport to close on Thursday. The backlog left passengers stuck on planes for long stretches while waiting for other aircraft to get in and out of gates.
Bitter cold is also disabling equipment on the tarmac.
Forecasters predicted ice accumulations from a band of freezing rain from Missouri through OH and Tennessee into the Mid-Atlantic, warning of hazardous road conditions before temperatures rise Monday.