At the Kearney Connection from Swift (MP 7.2), the NEC interconnects with the former Lackawanna line passing below it, with connectors on the north and south sides of the NEC for the use of NJT trains. There are four bridges over streets, dual road bridges high overhead, and five electrified tracks below and to the west (the Lackawanna line). The crossovers at Hudson (MP 8.6 from Penn Station/7.2 from the former terminal at Jersey City) are at the southwest end of the Waterfront Connection, which runs eastward from track 1 of the NEC to track 2 of the M&E at Meadows (MP 4.3 on that line). This track is used mostly eastbound on weekday mornings and westbound on weekday afternoons, with one reverse-commute trip in each direction. The PATH tracks come alongside to the south, climbing up from a lower level, and the most easterly two tracks of the NEC bridge over the westbound PATH track at this location
At Hudson, where there is water (the Hackensack River) alongside to the east/south and a tower on the west/north side of the main line, the number of tracks rises to three (with speeds 60-20) and then four (with speeds 45-20) the line from Meadows Yard (the former Jersey City line) also trails in from the east. There are also eight yard tracks at Hudson, used to store Amtrak MoW equipment, NJT equipment going to and from the NJT Meadowlands Maintenance Center, and Raritan Valley trains turning back to Newark Penn Station. The NEC and PATH lines turn gently towards the southwest, past the passenger station with two side platforms on the PATH tracks at Harrison (MP 8.3), with a bridge over a street in the platforms, across the Passaic River on parallel through truss bridges, including two at different levels for the PATH tracks, at the crossovers at Dock (MP 8.5), where speeds become 35-20, and into the passenger station at Newark Penn. (MP 8.8), with two side and three island platforms (all NEC stations in New Jersey have high-level platforms) serving six through tracks and two PATH tracks (one at an upper level), where the PATH service ends (the tracks continue a half mile further, bridging over the NEC to reach a storage yard on the west side.).
An overhead bridge at the south end of Newark Penn Station once carried the former CNJ Newark Branch over the NEC, requiring the southbound PATH tracks to descend steeply at the south end of their platform on the upper level.
From Newark, the NEC turns south-southwest, with speeds 70-20, past a bridge over a street, the PATH tracks climbing in the center, the overbridge carrying the tracks to the PATH storage yard to the west, three bridges over streets, signal bridges and crossovers at Cliff (MP 9.7), four bridges over streets, a road bridge overhead, and signal bridges and crossovers at Hunter (MP 10.5), where the NJT line departs to the southwest (a connection to the former Lehigh Valley), there is a through truss bridge carrying a line west, dual road bridges overhead, a passenger station with two island platforms and two through tracks in the center for Newark Airport, and a single track line trailing in from the east side, passing under the easternmost line (which rises up to accommodate this), carries the former Lehigh Valley freight line from Oak Island Yard.