The primary connection to both controlling systems was at Brownsville, Pennsylvania - with the south end of the P&LE's Pittsburgh, McKeesport and Youghiogheny Railroad and with the PRR's ex-Brownsville Railway. The PRR also interchanged traffic at Hoover, Pennsylvania, the end of its Coal Lick Run Branch. The B&O Railroad interchanged at Leckrone, Pennsylvania, and Rivesville, West Virginia.
The Monongahela Railroad was a joint venture of the Pennsylvania Railroad (PRR) and the Pittsburgh and Lake Erie Railroad (P&LE), both of which had plans to extend their lines in the area. Each company appointed four of their members to the board of directors, who held their first meeting in January 1901. The newly formed Monongahela Railroad acquired many lines in the area from the PV&C as well as the Southwest Pennsylvania Railway Company, as well as the 19 mile (30km) right of way from Brownsville to Adah from the PRR, for the sum of $519,696.13.
In 1905, the Dunlap Creek branch opened, which served several mines and coke works and also interchanged with the Baltimore and Ohio Railroad. The last move on this line was on November 6, 1975. The track was removed, and the real estate disposed.
In 1909, the Rush Run branch was constructed, and a patch town (Sarah, Pennsylvania) was constructed to house the workers at what would have been a coal mine. It was later determined, however, that the coal did not belong to the mine developer, and the line was abandoned, the town was scrapped. Only four trains ever ran on this line, those carrying the ballast to complete the track.
In 1910, the federal government condemned the low-clearance covered bridge in Bridgeport (now South Brownsville), and the Monongahela Railroad bought the bridge company and removed the bridge. In the same year, they installed a 10-stall roundhouse in Bridgeport. This was to be the main yard for the railroad throughout its history of operations.
In 1911, the railroad served seven mines and fifty one coke works (with 34 coke works and 1 mine being on the Dunlap Creek Dissivion) The daily rated output was 1,395 cars of coke and 280 cars of coal. In 1911-1912, the big push was the state line extension, to make a connection with the Buckhannon and Northern Railway (B&N). It involved a major river crossing, and two large creek crossings.
On July 1, 1915, the Monongahela Railroad consolidated with the Buckhannon and Northern Railway to form the Monongahela Railway Company (MRY), still under the control of the parent companies (PRR and P&LE).
In 1927 the Baltimore and Ohio railroad acquired 1/3 (1/6 from each the PRR and P&LE) of the capital stock of the Monongahela Railway, securing their interests in the coal producing area it served.
On November 25, 1952, the Monongahela Railway ran its first Baldwin S-12 diesel locomotive. This marked the beginning of the end of their fleet of steam locomotives, the last one of which being used on May 26, 1954.
In June 1968, the Waynesburg Southern Railroad Company (organized in the interest of the PRR) opened a line from Waynesburg to Consolidated Coal Company's Blacksville No. 1 mine and Eastern Gas & Fuel Company's Federal No. 2 mine. This line is still in service as of 2007.
On May 1, 1993, the Monongahela Railway was merged into the Consolidated Rail Corporation (Conrail), later to be bought by Norfolk Southern and CSX Transportation. Eleven GE Class B23-7Rs (sometimes referred to as Super 7s) numbered 2300-2310 were renumbered 2030-2040 by Conrail.
In 1903 six class H3-A 2-8-0 locomotives were purched from the PRR, numbered 201-206. six class G-1 2-8-0 steam locomotives were purchased from the P&LE, numbered 101-106.
Between 1904 and 1905, two class D-3 4-4-0 steam locomotives were purchased from the PRR, numbered 301 and 302.
Between 1905 and 1906, two class H-1 2-8-0 steam locomotives were purchased from the PRR, numbered 107-114.
In 1907 six class H-4 2-8-0 steam locomotives were purchased new from the PRR (built for MRR), numbered 207-212.
In 1909 two class D-1 4-4-0 steam locomotives were purchased from the P&LE, numbered 300 and 301.
Between 1909 and 1913, steam twenty-six class H-5 2-8-0 locomotives were purchased from ALCO, numbered 115-140.
In 1911 two class D-4 4-4-0 steam locomotives were purchased from the P&LE, numbered 303 and 304.
Between 1915 and 1916, three class D-4A 4-4-0 steam locomotives were purchased from the P&LE, numbered 305-307.
Between 1915 and 1917, twelve class H-5SA 4-4-0 steam locomotives were purchased from ALCO, numbered 141-152.
Between 1917 and 1918, three class E-2A 4-4-2 steam locomotives were purchased from the PRR, numbered 308-310.
Between 1917 and 1918, ten class L-1 2-8-2 steam locomotives were purchased from ALCO, numbered 170-179.
In 1923 one class H-5SA 2-8-0 steam locomotive was purchased from H.K. Porter Co., numbered 153.
In 1926 two wrecked class G-1 4-6-0 steam locomotives (No. 34 and 35) were purchased from the Scotts Run Railway Company and rebuilt, one renumbered 99.
In 1927 six class L-2 2-8-2 steam locomotives were purchased from Baldwin, numbered 180-185.
In 1937 one class E-3SD 4-4-2 steam locomotive was purchased from the PRR, numbered 311.
In 1940 three class L-3 2-8-2 steam locomotives were purchased from the P&LE, numbered 186-188.
Between 1941 and 1944, five class L-3A 2-8-2 steam locomotives were purchased from the P&LE, numbered 189-193 (189 and 190 formerly LE&E equipment).
Between 1947 and 1949, seven class L-3B 2-8-2 steam locomotievs were purchased from the P&LE, numbered 194-200 (194-201 formerly PMcK&Y equipment).
Between 1950 and 1969, twenty-seven class S-12 4-4 diesel locomotievs were purchased from Baldwin-Lima Hamilton, Eddystone division, numbered 400-426. In addition nine locomotives built by Baldwin-Lima Hamilton were acquired from Penn Central, seven class RF-16 diesels numbered 1205-1216, and two RF-16B diesels numbered 3708 and 3709. (note: 3709 was never used)
Between 1970 and 1989, five class GP-38 4-4 diesel locomotives were purchased from the Electric-motive division of general motors, numbered 2000-2004. In addition, nine class GP-7 4-4 diesel locomotives were purchased from the P&LE, six in 1974 and three in 1975 to replace three that were wrecked, numbered 1500-1510.
Between 1990 and 1993, eleven class B23-7Rs 4-4 diesel locomotives were purchased from General Electric, remanufactured from former Western Pacific units, numbered 2300-2310.