NEW YORK >> After Tropical Storm Irene forced an unprecedented closure of the nation’s largest mass transit system, New York City subways resumed service Monday with a major test as millions of commuters ventured to work for the first time since the storm hit.

Limited service resumed at 5:40 a.m., and Metropolitan Transportation Authority spokesman Charles Seaton said subways were running smoothly, if a little more slowly than usual. He said commuters could expect a bit more crowding but otherwise service was normal.

Metro-North Railroad, which serves the city’s northern suburbs, was reopening on a limited basis Monday afternoon. New Jersey Transit trains were also suspended, but the system’s light rail and buses were operating.

Riders who expected a difficult commute said they were relieved.

"The subway is running very well. I can’t believe it, they did a great job," said Dominic Cecala, who took an E train from the city’s west side to lower Manhattan. "If they hadn’t stopped the trains on Saturday, it would have been a mess."

The MTA’s decision to halt all subways, buses and commuter trains in preparation for the storm — the first time a natural disaster ever closed the system down — had threatened to disrupt the start of the work week in the nation’s most populous metropolitan area.

Long Island Rail Road was dealing with storm-related service disruptions. Five of LIRR’s 11 lines were suspended and the others were experiencing delays of up to an hour.

PATH trains in and out of the city from New Jersey were operating on a normal schedule. Greg Kurilli, an electrician who works in lower Manhattan, arrived at the World Trade Center PATH station from Jersey City on time.

"I hope I won’t be working anywhere near the water," he said.

Ferries to and from Staten Island were running well. Joe Dinguis, a 56-year old career counselor, expected problems getting from his home in Staten Island to his job in Brooklyn. But as he disembarked from the ferry in lower Manhattan, he said his trip had gone smoothly so far.

"Everything’s fine today," including the Staten Island Railway, he said.

Things weren’t quite as fine for some New Jersey Transit commuters and those in the Westchester suburbs.

With Metro-North service suspended during the morning commute, Westchester residents attempting to drive into the city were stymied by the numerous roads and parkways that had been closed because of flooding.

At New York’s Penn Station, commuters hoping to take New Jersey Transit were surprised to learn it was still shut down.

"I got here and it was closed. I’ve got to call my boss," said Rosa Carrasquillo of Perth Amboy, N.J. "I was shocked, I don’t know what happened. I really need to get to work today."

The center of Irene passed over Central Park at midmorning Sunday packing 65 mph winds, but damage to New York City was less than feared. An evacuation order for low-lying city neighborhoods was lifted Sunday afternoon. By Sunday night, limited bus service started up.

With a daily ridership of more than 5 million, New York City’s subway system is by far the nation’s largest. Many New Yorkers do not have cars and would be hard-pressed to get around without the subway.

The MTA had done simulated runs throughout the subway system in order to be ready for Monday’s commute.

"Suspending service allowed the MTA to secure equipment, thus expediting the return to service," New York Gov. Andrew Cuomo said in a statement.