The tracks carry Long Island Rail Road (LIRR) and Amtrak trains travelling to and from Penn Station and points to the north and east.

They are part of Amtrak's Northeast Corridor, used by trains traveling between New York City and New England via the Hell Gate Bridge.

The original plan for the extension which was published in June 1901, called for the construction of a bridge across the Hudson River between 45th and 50th Streets in Manhattan, as well as two closely spaced terminals for the LIRR and Pennsylvania Railroad (PRR).

This would allow passengers to travel between Long Island and New Jersey without having to change trains; at the time, LIRR trains ran to Long Island City, where passengers took ferries across the East River to the 34th Street Ferry Terminal in Manhattan.

The PRR and LIRR lines would converge at New York Penn Station, an expansive Beaux-Arts edifice between 31st and 33rd Streets in Manhattan.

New Haven trains began running through the East River Tunnels, serving Penn Station, in 1917 after the Hell Gate Bridge opened.

However, due to delays in the East Side Access project (which would give LIRR riders a second direct route into Manhattan via the 63rd Street Tunnel), Amtrak later pushed back the start date of the East River Tunnels' reconstruction to 2025, and increased the construction time to four years.

[21] Amtrak hired Skanska E-J ERT Joint Venture in July 2024 to repair the tunnels for about $1.6 billion.