NEW YORK (AP) — New York City’s subway system was fully operational for the Tuesday morning commute, however some roads remained closed in sections of New York and New Jersey after heavy rain swept across the U.S. Northeast overnight, causing flash floods.

Dozens of flights were delayed or canceled at area airports Tuesday, including 159 total cancelations at Newark Liberty Airport, according to FlightAware data.

Most flash flood watches and warnings had expired in parts of New Jersey, New York and Pennsylvania as the rain moved on, but a state of emergency declared by Gov. Phil Murphy remained in New Jersey, where video on social media showed cars still partially inundated in some parts of the state as residents worked to clean up.

Delays were reported on part of the state’s commuter rail line due to the severe weather.

In New York, however, Janno Lieber, chair and CEO of the Metropolitan Transit Authority, told ABC 7 in New York there was now full subway service, as well as full Long Island Railroad and Metro North commuter rail service after hundreds of people worked overnight to restore operations.

Video posted on social media appeared to show water flooding down into a Manhattan subway station, submerging the platform while passengers inside a train watch. Another photo appears to show passengers standing on a train’s seats to avoid the water beginning to soak the floor.

Lieber said the city’s sewer system got overwhelmed by the rain and backed up into the subway tunnels and to the stations. In several cases, he said, the backup “popped a manhole,” creating the dramatic “geyser” seen in some videos.

“What happened last night is something that is, you know, a reality in our system,” he told the TV station, noting the backup happens when more than 1 3/4 inches of rain falls in an hour. “We’ve been working with the city of New York to try to get them to increase the capacity of the system at these key locations.”

In one flooded neighborhood in North Plainfield, New Jersey, authorities were investigating why a house caught on fire and collapsed and whether it was due to a possible explosion. It occurred not long after the family inside had evacuated, authorities said. No injuries were reported.