Several issues have led to delays and cancellations for about a week, and those disruptions were happening again Monday morning.
United Airlines announced it would cancel 35 round-trip flights daily, a necessary step, the company said, to protect its customers.
This, after United Airlines said more than 20% of FAA controllers at Newark walked off the job.
Without them, Newark cannot handle the number of planes scheduled to operate there in the weeks and months ahead.
In addition to staffing limitations, officials say air traffic control outages have contributed to the ongoing problems at Newark Airport over the last week.
Runway construction is another problem that has left this airport with just one runway.
In the meantime, mounting delays and cancellations meant missed connections for some travelers.
"Three hours for us, but I don't know, they need a pay raise, whatever. I think they should get what they're asking for," one traveler said.
"We kind of came in having no idea it was happening, but it looks like everyone's getting hit by it," said Cameron Olivier, a traveler to Canada.
With the summer travel season just weeks away, the Department of Transportation has been trying to find solutions, including rolling out a plan to hire more air traffic controllers and delay retirement.
Officials are expected to announce another plan this week to modernize air traffic control technology.
Newark Airport has put out a travel advisory, urging passengers to check their flight status before heading to the airport.