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Active freight rail yards in New York City and Long Island
- 65th Street Yard – Brooklyn shore, reopened in 2012 after being refurbished for cross harbor car float
- Arlington Yard – small yard servicing Staten Island
- Brookhaven Rail Terminal – new (2011) facility for bulk commodities, in eastern Long Island
- Harlem River Intermodal Yard – the Bronx, intended for intermodal container traffic, used for trash containers instead
- Bush Terminal (Industry City) – Brooklyn shore, used for car float operations
- Hunts Point Terminal Market – Bronx, largest food distribution center in New York
- Fresh Pond Junction – Queens, main freight yard on Long Island, hub of NY&A
- New York Container Terminal – Staten Island, includes an intermodal rail yard
- Oak Point Yard – Bronx, largest freight yard in the City, owned by CSX.
- Pine Aire Yard in Farmingdale, owned by NY&A and used to serve industries along the LIRR Main Line.
The New York City Subway system has many other rail yards, but, with two exceptions, these are not connected with the national rail network. See South Brooklyn Railway