Some electric trains terminate at South Amboy and make all stops from New York Penn Station, providing local service for the Northeast Corridor stops of Rahway, Linden, Elizabeth, and North Elizabeth during rush hours.

Bay Head contains a large balloon (circular looping) track where entire trains can reverse direction without backing up or uncoupling the locomotive, and obviating the need for a turntable.

The line also crosses over several other waterways on fixed bridges, the longest of which is over the Navesink River at Red Bank.

On May 18, 2015, NJ Transit expanded service to include three inbound and three outbound weekday trains running from Bay Head directly to and from New York Penn Station.

The line was home to the last remaining private commuter passenger club in the United States.

In 2004, the Comet II Club Car went through a custom overhaul by Alstom and was furnished, with the club's funding, to include reclining lounge chairs, spacious seating, at-seat fold down tables, and private conference tables.

In the summers of 1986–1988, NJ Transit experimented with service from selected stops of the Bergen County Line, around the southwest curve of the West End Junction in Jersey City, and switching from the Morris & Essex to the Northeast Corridor via a complicated set of switch maneuvers in the Newark area, then continuing express to the Coast Line, with no intermediate stops between Harmon Cove station and Long Branch station.

[1] In June 2014, NJ Transit began running one-seat limited-stop summer shore express trains to and from Bay Head and New York on weekends and holidays.

The Raritan Bay and Morgan Creek drawbridges were struck by boats, storage containers and other floating debris, knocking the bridges' tracks out of alignment.

Between New York and Long Branch service is typically operated with an ALP-46 electric locomotive pulling Comet or MultiLevel coaches.

Shuttle trains between Long Branch and Bay Head are typically operated with a PL42AC or GP40PH-2B diesel locomotive pulling 4 to 6 car sets of Comet series or MultiLevel coaches.

During weekday rush hours, NJ Transit operates "One Seat Ride" services between New York and Bay Head.

These trains use ALP-45DP dual-power locomotives that can run on either electric power supplied by overhead lines or from an on-board diesel generator.

NJ Transit also operates short turn runs between New York and South Amboy during weekday rush hours.