Amtrak says it's not clear when service will return along the Northeast Corridor between Boston and Philadelphia.
By Monday afternoon, flood waters still remained on the tracks in Trenton. The tracks were submerged by water from the Assunpink Creek, which Hurricane Irene raised to record levels.
Amtrak spokeswoman Danelle Hunter says the rail line is also dealing with power issues in some areas. And crews were working to remove trees and other debris that got pushed on the tracks.
Amtrak isn't alone in their transit troubles, Hurricane Irene is to blame for many SEPTA service interruptions as well.
It was limited service and cancellations across the board for SEPTA's Regional Rail lines.
The storm flooded, left debris, and caused power outages along the Paoli/Thorndale, Cynwyd and Trenton lines.
Since all three lines run on Amtrak tracks, they must be checked before service can restart.
"In Trenton, there was a lot of flooding and downed lines so Amtrak has to access the situation and see if the water has receded yet," said Heather Redfern of SEPTA.
According to SEPTA, the Paoli/Thorndale and Cynwyd lines are scheduled to resume service Tuesday.
Amtrak is currently assessing the damage from Hurricane Irene. Once that process is complete, test trains must be sent out before operations are set to resume.