The station is served only during weekday rush hours in the peak direction (to Long Island City in the morning, from Long Island City in the evening) by diesel trains from the Oyster Bay, Montauk, or Port Jefferson Branches via the Main Line. There is a connection to the Lower Montauk Branch, but as of November 2012[update], no LIRR trains run on that branch, which is now leased to and controlled by the New York and Atlantic Railway, which uses the line exclusively for freight operations.
This station was built on June 26, 1854, and rebuilt seven times during the 19th Century. On December 18, 1902, both the two-story station building and office building owned by the LIRR burned down. The station was rebuilt on April 26, 1903, and electrified on June 16, 1910.
Before the East River Tunnels were built, this station served as the terminus for Manhattan-bound passengers from Long Island, who took ferries to the East Side of Manhattan. The passenger ferry service was abandoned on March 3, 1925, although freight was carried by car floats through Gantry Plaza State Park to and from Manhattan until the middle 20th century. Today, ferry service is operated by NY Waterway. The station house was torn down again in 1939 for construction of the Queens–Midtown Tunnel, but still continued to operate as an active station, as it does today.
This station has 13 tracks, two concrete high-level island platforms, and one wooden high-level island platform. All platforms are two cars long and accessible from Borden Avenue just west of Fifth Street. The other concrete platform adjacent to tracks 6 and 7 and the wooden one adjacent to tracks 8 and 9 are used for employees only. All tracks without platforms are used for train storage. The southernmost four tracks are powered by third rail while the remaining tracks are used only by diesel-powered trains.