The M&E operates four freight rail lines in northern New Jersey. These freight lines are bridged by M&E trackage rights on NJ Transit commuter lines, creating a combined M&E system of over 150 miles of track. Freight is interchanged with Norfolk Southern at Lake Junction in Wharton, NJ and with CSX in Kearny, NJ. Additionally, the M&E’s Bayshore Terminal Company provides in-plant switching for the Bayway Refinery in Linden, NJ.


The Whippany Line is a 9-mile rail line, owned and operated continuously by the M&E since the railroad’s inception in 1895. The line runs east from Morristown through Hanover Township and East Hanover to its end in Roseland. The Whippany Line has several transload sites available for transloading with close access to Route I-287. This rail line is also the home of the M&E’s mechanical shop and corporate offices in Morristown.


The Chester Branch is a 3.6-mile branch operated for Morris County (and previously for the Chester Branch Company) by the Morristown & Erie since 1983. The branch begins at Lake Junction, which is the location of the M&E's main interchange with Norfolk Southern. It continues southwest through Ferromonte Junction and ends in Randolph.


The Dover & Rockaway Branch is a 6.2-mile branch operated for Morris County by the Morristown & Erie since 1986. The branch starts at D&R Junction (on NJ Transit just west of Dover) and continues east through downtown Dover, paralleling the NJ Transit main line. It passes through both Rockaway Borough and Township to the end of the line, which is located just east of US Route 80. A transload facility suitable for high-and-wide loading is located in Rockaway.


The High Bridge Branch is a 7.3-mile branch operated for Morris County by the Morristown & Erie since 1986. The branch starts at Ferromonte Junction (where it connects to the Chester Branch) and travels through the towns of Roxbury, Mount Olive, and Flanders. There is a transload facility with a loading dock available in Kenvil.