All MTA lines appeared to be running smoothly as the morning rush got under way Tuesday as NJ Transit and Metro-North continued the challenging process of getting back on track.
Damage from Irene had kept the commuter rails from coming back as fully as the New York City subway system, which was up and running back to normal Monday after having been shut down for the first time in a natural disaster.
NJ Transit riders experienced delays of up to 30 minutes on the New Jersey Coast line and the Raritan line.
New Jersey Transit rail passengers should expect delays as the commuter railroad restores Northeast Corridor service from Trenton to New York City Wednesday.
There are ongoing signal problems because of earlier flooding in Trenton that halted service at New Brunswick.
NJ Transit says Northeast Corridor trains are subject to delays up to 15 minutes.
North Jersey Coast Line trains can be up to 15 minutes late. There's no rail service at Bound Brook because of flooding on the Raritan valley Line.
Rail service on the Port Jervis Line is suspended between Suffern and Harriman.
NJ Transit will restore service on the Montclair-Boonton line between Little Falls and Mountain Lakes this afternoon. That stretch of the line had been suspended due to flooding.
Passengers should check schedules.
Only two of the LIRR lines were still suspended Tuesday afternoon, covering the eastern end of Long Island.
The LIRR said it planned to restore full weekday service on the Long Beach and Port Jefferson branches for the Wednesday morning rush. Those two branches were the only ones that remained suspended Tuesday evening.
For Metro-North, officials said 85 percent of its morning peak customers would be able to get trains, with the restoration of the entire Hudson and New Haven main lines and the Harlem line up to North White Plains.
Service on the Waterbury Branch resumes today, though customers should expect delays of 20 to 40 minutes because of utility power outages affecting grade crossings. Regular weekday service is in effect on the Harlem Line (to and from Southeast), Hudson Line, New Haven Main Line, and New Canaan Branch.
Busing is in effect on the Upper Harlem (Southeast to Wassaic). Service was still suspended on the Danbury line.
The damage to Metro-North's system from Irene was severe, said MTA spokeswoman Marjorie Anders. "It's worse than anything we had ever seen," she said. Restoring some parts, on the Port Jervis line above Suffern, N.Y., would take months, she said.
Most Amtrak train service between Washington and Boston was restored by Tuesday night. For the most recent updates, check Amtrak's Facebook page.