The rail service says repairs have been made but there will be delays when trains start running again.
(DEVELOPING... EARLIER STORY BELOW)
In a region where commuters depend on trains, New Jersey Transit and the Philadelphia transit system also could not get their trains into Trenton.
The flooding left commuters to work from home, business travelers to hope they could make their meetings and many people scrambling for seats on buses.
Gilean Denny, 27, who is working on a Ph.D. in architecture at the University of Cambridge in England, was trying to get from her parents' home in Philadelphia to New York in time for a job interview.
At midday, it wasn't promising. Trains weren't running. Megabus, which has a stop across the street from Philadelphia's 30th Street Station, was full.
Even if she could get a seat, Denny, wearing a suit for the interview, worried about a bus breakdown - something she's experienced before.
"It'll add to the humor of the day," she said.
The chokehold on one of the busiest parts of the nation's passenger rail service was caused by the Assunpink Creek, a waterway so small you might not notice it under normal conditions. On Sunday, it spilled out of its banks and turned the station into a pond, partly submerging trains parked there.
The water receded and was off the tracks by Tuesday morning, but Amtrak spokeswoman Danelle Hunter said service would not immediately resume. She said officials at the federally subsidized train service hoped that by later Tuesday, they would at least have a sense of what repair work needed.
Sean Jeans-Gail, vice president of the National Association of Railroad Passengers, said his group did not fret about disruptions caused by flooding on the Assunpink before Irene and was not especially worried about it after. Since most service suspensions are caused by equipment failures, Jeans-Gail said Amtrak has higher priority projects that would keep the trains running reliably.
But he said this week's problems may be a wake-up call.
"If climate change is going to affect the kind of storms we get in the Northeast, it certainly is something transit officials need to look at," he said.
In the meantime, more than 17,000 passengers who usually hop on New Jersey Transit and Southeastern Pennsylvania Transportation Authority trains in Trenton and two nearby stations needed to change their plans, along with many more whose Amtrak travels take them between New York and Philadelphia.
Amtrak was only able to run trains between New York City and Boston and between Philadelphia and Washington, D.C., leaving an approximately 90-mile hole in the middle of its popular Northeast Corridor routes.
Officials at the discount bus lines Megabus.com, owned by Coach USA, and BoltBus, a division of Greyhound Lines, said they had more riders than usual over the last few days. But the train outages were seen as just one reason. There was also pent-up traffic from when Irene shut down roads and people who evacuated as Irene approached were trying to get back home.
Rob Gonci, 45, of Akron, Ohio, needed to get from New York City to Philadelphia for a business meeting, so he was on a sidewalk with his briefcase, trying to figure out how to purchase a bus ticket. His train had been canceled Tuesday morning after he flew in the night before.
"Do you book a hotel another night, and then tomorrow the trains still aren't going?" he wondered. "Or do you just cut your losses?"
For Raleane Fisher, the frustration ran deep. The 43-year-old police officer from Perth, Australia, is touring the U.S. and had a lot of headaches after she learned her train to Philadelphia was canceled. She was on the phone Tuesday trying to get a refund from Amtrak while waiting for a BoltBus to show up.
"Now we've got a bus which is half an hour late," she said, "and we don't even know if we're getting on that."
Washington attorney Betty Sinowitz was at New York's Penn Station on Tuesday afternoon coming to grips with the limited options available to her. She thought she might take a bus, but couldn't get a through for a phone reservation.
"I'm a game player, and I like to find strategies, but there's no game left to play here," she said.
Amtrak says some of its Empire Service train service between Albany and New York City is set to resume after being shut down by Tropical Storm Irene.
The passenger railroad says trains should be running after 4 p.m. Tuesday.
Customers can check schedules online or by phone for more details.
Passengers are encouraged to call 800-USA-RAIL or visit Amtrak.com for schedule information and train status updates.