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.

[8] 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.

[9] By the 1970s, a new bypass was being proposed[10] because of the clearance and tight curves of the Port Morris Branch's tunnels, which could not fit contemporary train cars.

[13] The rest of the track bed had a sizable homeless and drug-dealer encampment,[14] was strewn with garbage,[11][15] and is frequently flooded due to the poor drainage and its location below sea level.

[11] 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,[16] was pumped in 2009 for $350,000, although the garbage was allowed to remain.