[2] Instead, the line started at a point named Annapolis Junction near Savage Factory, near milestone 18 on the Washington Branch.

There were trestles spanning Chandlers Run and Rouges Harbor Branch and an excavation at Magazine Hill, just east of Waterbury.

The Union's Massachusetts Infantry was moving south to secure Washington, D.C., but Maryland, a slave state, contained many southern sympathizers and when the troops attempted to march through the city the Baltimore riot of 1861 broke out.

On April 21, 1861, the telegraph lines, railroad engine and many sections of track had been torn up by Marylanders dissatisfied with the outcome of the riot.

In October 1879, the Maryland Board of Public Works began to investigate why, in 40 years, the railroad had not paid any of the interest on the state's $300,000 investment.

The A&ER management blamed competition from ferry boats and high interchange tariffs charged by the Baltimore and Ohio.

The state attempted to prevent the sale, but in July 1885 the injunction they had obtained was dissolved and on November 10 of that year the Annapolis and Elkridge Railroad was sold for $100,000.

It provided a faster connection from Annapolis to Baltimore as it took a more direct path along the north shore of the Severn River.

The AW&B was closed and then reopened in 1908 with electric passenger rail between Naval Academy Junction and Annapolis and steam engines used to haul freight.

[14][15] The installation was supposed to be a temporary facility, used only for the duration of the war, but it became Fort Meade, a permanent establishment, in 1928 and is still in use today.

In 1943, a cabinetmaking company, later National Plastics moved into the old WB&A shops at Academy Junction and used the rail line.

[12] It dropped again when the 1st Squadron, 6th Cavalry Regiment which regularly required the movement of tanks and artillery by rail left Fort Meade.

[16] In December 1982 all rail operations to Fort Meade ceased and the base's single locomotive, an 80-ton diesel built by General Electric in 1952 and numbered 1684, left for Baltimore (pulling up the track behind it) and then the McAlester Army Ammunition Plant in Oklahoma.

[12][18] The rail remained there until the Patuxent Freeway was built in 1989, at which time the line was broken on the west side of Fort Meade.

[18] The tracks west of Academy Junction continued to be used to serve the National Plastics, later Nevamar, factory in Odenton, but saw an end to regular use after it closed in 2004.