A major transportation headache could be in store for Long Island Rail Road riders, as Amtrak moves forward with plans to shut down one of the four East River tunnels that connect to Penn Station. The long-anticipated rehabilitation project is aimed at repairing damage caused by Superstorm Sandy—but MTA officials are warning it could severely disrupt commuter service.

Amtrak, which owns and maintains the tunnels, will close one tunnel entirely starting May 9, with the project expected to last into next year. Once that tunnel reopens, another will be taken offline for similar repairs, continuing the cycle until at least 2027.

LIRR commuter Thaddeus Smith is bracing for a challenging few years.

“That’s going to be horrible for us,” he said.

Currently, the LIRR operates with all four East River tunnels. But one is occasionally forced to close because of an emergency.

Officials warn that having only three tunnels available leaves little room for flexibility or incident response.

Marc Herbst, an MTA board member, warned of the possibility of extensive service disruptions.

“If they shut these tunnels down and there’s an incident, the risk has just increased tremendously that we’re going to have further delays," he says.

The MTA has urged Amtrak to complete the work during overnight and weekend hours to minimize the disruption.

However, Amtrak’s leadership is defending the decision and the timeline. In a written statement, Amtrak President Roger Harris said the plan was approved months ago by the MTA and remains the most “efficient, reliable, and timely” way to complete the full rehabilitation.

Amtrak has indicated it is moving forward with the closure, despite pushback.