The IRT resumed work in 1905 and completed the tubes in 1907 and was briefly opened for trolley service that September.

In subsequent years, specific rolling stock were ordered to navigate the narrow dimensions of the tubes, and the tunnel suffered from numerous floods and fires.

[5] The East River Tunnel Railroad Company soon dissolved, and on July 22, 1887, Walter S. Gurnee and Malcolm W. Niven founded the New York and Long Island Railroad Company (NY&LIRR), which began planning for the tunnel shortly afterward.

In July 1891, piano maker William Steinway, a major landowner in Astoria, Queens, started to fund the tunnel.

[5] Construction was started on June 7, 1892, as a NY&LIRR project, and the bottom of the tunnel shaft was reached in December of the same year.

The project was difficult due to complex geological formations beneath the river, and there were frequent blowouts and floods.

[6]: 164–165 [8] Due to high compensation claims, the company was financially ruined, and attempts to raise additional funds failed because of the stock market crash of 1893.

[5] In 1900, the Interborough Rapid Transit Company (IRT), headed by August Belmont Jr., was awarded the contract for construction and operation of the city's subway line and a few years later the IRT engineered a takeover of Manhattan's elevated railways, thus gaining a monopoly on the city's rapid transit services.

The tunnel was to turn at a loop at the corner of 42nd Street and Park Avenue in Manhattan and go as far as Vernon Boulevard in Queens.

Shaft #3 was sunk in the Man-O-War Reef, a granite outcrop in the East River that was expanded and renamed Belmont Island.

The concession to operate the tunnel had expired on January 1, 1907, and the city of New York was unwilling to renew the contract.

[5][6]: 168 Initially, the IRT intended to use the tunnel for trolleys;[6]: 165  however, it subsequently decided instead to use the tubes for a heavy-rail rapid transit line, a concept that later became known as premetro.

The roadbed and the rail were determined to be usable for subway service, but even so, the duct banks in the tunnel were replaced.

The work included removing part of the tunnel walls on the Manhattan side and building a cavern to create a track crossover between the tubes.

[12] The planned metro route was to go from Times Square through the tunnel over to Long Island City and from there continue towards Flushing.

Hunters Point Avenue opened on February 15, 1916, and on November 5 of the same year, it was extended to Queensboro Plaza.

Because the line did not have track connections to the rest of the IRT network, a provisional maintenance workshop was operated at the tunnel ramp until 1928.

[5] With the 1948 introduction of four-motor subway cars of types R12 and R14, the need for a special drive was gone, as the Steinway Tunnel could now be driven by conventional railcars.

[23] After Hurricane Sandy-related storm surges flooded the tunnel in 2012, the tubes were rebuilt in a $29 million project that took place between 2013 and April 2016.