[5]: 111, 114  The B&O used trackage rights on the PW&B to operate trains to Philadelphia and Jersey City starting at about this time.

Although the PW&B was an independent company at the time, the use of key sections of track in Philadelphia and New Jersey depended upon the cooperation of the Pennsylvania Railroad (PRR).

B&O began planning immediately for its own line between Baltimore and Philadelphia, where a connection to the friendly Reading Railroad would provide access to the New York area.

[4]: 26–29 [6] B&O passenger trains continued crossing the river on the PW&B until the trackage rights agreement expired on October 12, 1884.

B&O's new line, the Baltimore and Philadelphia Railroad, was built to higher engineering standards than typical on its system, despite the company's shaky finances.

The foundations for six of the piers have been difficult, reaching, as they do, a depth of 85 feet [26 m] below low water, and necessitating the use of caissons, with air chambers, in which the men, engaged in removing the debris in order to reach bed-rock, have worked under a pressure of 37 pounds per square inch [260 kPa].

[4]: 39–41, 43, 75–76 In the early years of the 20th century, the iron bridges on the Philadelphia line could no longer handle the latest locomotive designs at optimal speeds.

The crane collapsed, bringing down the eastern channel through truss, which sank in deep water.

[4]: 170–175 As of 2006[update], CSX runs about 24 trains daily on the Philadelphia Subdivision, including intermodal, autorack, and general merchandise freights.