The Port Morris Branch began at a wye north of Melrose Station, then extended southeast through The Hub, through a 2,200-to-2,300-foot-long (671 to 701 m) tunnel (built 1905) under St. Mary's Park, and finally Port Morris along the East River just after crossing a bridge beneath the Harlem River and Port Chester Branch of the New York, New Haven and Hartford Railroad.
A connecting wye existed partially beneath the bridge lead to the New Haven Railroad-owned Oak Point Yard as well as the HR&PC itself.
The only two stations along this branch were at Westchester Avenue between Brook and St Ann's Avenues 40°48′57″N 73°54′46″W and at Port Morris itself across the river from North Brother Island.

After World War II, the Port Morris Branch faced decades of underutilization and the increase in poverty and rampant violence from the surrounding neighborhoods, as well as low clearance and poor drainage.
By the 1970s, a new bypass was being proposed because of the clearance and tight curves of the Port Morris Branch's tunnels, which could not fit contemporary train cars.
After the construction of the Oak Point Link at the Bronx's southern tip and its subsequent opening in 1998, the Port Morris Branch ceased to be used in 1999; formal abandonment was declared in 2003, when CSX Transportation declared that the branch could be vacated due to the lack of use in the preceding two years.
The Oak Point Yard remains just northeast of the site of the port, and an industrial track in the vicinity of the Port Morris station still survives south of Southern Boulevard.
The rest of the track bed had a sizable homeless and drug-dealer encampment, was strewn with garbage, and is frequently flooded due to the poor drainage and its location below sea level.

The "Mott Haven Swamp," as the corridor was called in the late 2000s due to the 625,000 US gallons (2,370,000 l; 520,000 imp gal) of stagnant water inside the trench, was pumped in 2009 for $350,000, although the garbage was allowed to remain.
It is unknown who had owned the track bed, though different sections had been purchased by several private organizations.

Restoration was proposed in 2014, to connect the Harlem Line to an expanded LaGuardia Airport.
In 2015 the homeless encampment was vacated and bulldozed.
Afterward, another plan was made to connect the spur to the Harlem Line and to the New York Connecting Railroad as part of a New York City Subway circumferential line called Triboro RX.
However, these plans were complicated due to the private ownership of the land next to the right-of-way, as well as a new housing development directly on the right-of-way at 156th Street.
The Port Morris Branch began at a wye north of Melrose Station, then extended southeast through The Hub, through a 2,200-to-2,300-foot-long (671 to 701 m) tunnel (built 1905) under St. Mary's Park, and finally Port Morris along the East River just after crossing a bridge beneath the Harlem River and Port Chester Branch of the New York, New Haven and Hartford Railroad. A connecting wye existed partially beneath the bridge lead to the New Haven Railroad-owned Oak Point Yard as well as the HR&PC itself. The only two stations along this branch were at Westchester Avenue between Brook and St Ann's Avenues 40°48′57″N 73°54′46″W and at Port Morris itself across the river from North Brother Island.
After World War II, the Port Morris Branch faced decades of underutilization and the increase in poverty and rampant violence from the surrounding neighborhoods, as well as low clearance and poor drainage. By the 1970s, a new bypass was being proposed because of the clearance and tight curves of the Port Morris Branch's tunnels, which could not fit contemporary train cars. After the construction of the Oak Point Link at the Bronx's southern tip and its subsequent opening in 1998, the Port Morris Branch ceased to be used in 1999; formal abandonment was declared in 2003, when CSX Transportation declared that the branch could be vacated due to the lack of use in the preceding two years. The Oak Point Yard remains just northeast of the site of the port, and an industrial track in the vicinity of the Port Morris station still survives south of Southern Boulevard. The rest of the track bed had a sizable homeless and drug-dealer encampment, was strewn with garbage, and is frequently flooded due to the poor drainage and its location below sea level.
The "Mott Haven Swamp," as the corridor was called in the late 2000s due to the 625,000 US gallons (2,370,000 l; 520,000 imp gal) of stagnant water inside the trench, was pumped in 2009 for $350,000, although the garbage was allowed to remain. It is unknown who had owned the track bed, though different sections had been purchased by several private organizations.
Restoration was proposed in 2014, to connect the Harlem Line to an expanded LaGuardia Airport. In 2015 the homeless encampment was vacated and bulldozed. Afterward, another plan was made to connect the spur to the Harlem Line and to the New York Connecting Railroad as part of a New York City Subway circumferential line called Triboro RX. However, these plans were complicated due to the private ownership of the land next to the right-of-way, as well as a new housing development directly on the right-of-way at 156th Street.
Spuyten Duyvil and Port Morris Railroad