In 1937, the State Roads Commission was authorized to construct tunnels financed by tolls to be collected on the completed projects (Chapter 356, Acts of 1937). Now, State tunnels are the responsibility of the Maryland Transportation Authority of the Department of Transportation. All are found around Baltimore City.

Baltimore Harbor Tunnel. This tunnel opened in November 1957 between Canton and Fairfield. Designated I-895, the 1.4-mile, four-lane tunnel provided the first direct link north and south under the Harbor for vehicles bypassing Baltimore City. When it opened, the Harbor Tunnel was the longest twin-tube trench tunnel in the world.

Fort McHenry Tunnel. In 1985, this eight-lane tunnel became a vital part of I-95, the East Coast's most important interstate route. The Tunnel crosses under the Patapsco River south of Fort McHenry, and connects the Locust Point and Canton areas of Baltimore City.

Electronic toll-collection (known as M-TAG) began for both tunnels in 1999. In January 2003, M-TAG became part of the E-Z Pass system. Tolls of $4.00 each way for cars ($3 for E-Z Pass users & higher for vehicles with 3 or more axles) are collected electronically for both tunnels.

Baltimore and Potomac Tunnel. For commuters and intercity rail passengers traveling north and south, their route passes through tunnels under Baltimore City. The 1.4 mile long Baltimore and Potomac Tunnel was built in 1873 by the Pennsylvania Railroad and consists of three short tunnels: Gilmore Street, Wilson Street, and John Street. It connects Pennsylvania Station to Washington and Virginia. Also constructed in 1873, the Union Tunnel connects Pennsylvania Station to the main line heading to Philadelphia and points north. Lying just east of Baltimore's Penn Station, the Union Tunnel is about 0.6 miles long. Both tunnels are owned by Amtrak.

On January 30, 2023, President Joseph R. Biden, Jr. visited Baltimore to kick off the Baltimore and Potomac Tunnel Replacement Program. The B&P Tunnel, the oldest tunnel on the busy Northeast Corridor, will be replaced by the Frederick Douglass Tunnel, which is scheduled to open in 2032. The modern, four-mile-long section will include two tubes for electrified passenger trains, new track and signalling systems, five new bridges and roadway, as well as a new ADA-accessible West Baltimore MARC station. Freight trains will continue to use the original tunnel for the time being.

Howard Street Tunnel. Completed in 1895 and listed on the National Register of Historic Places, the Howard Street Tunnel serves commercial freight trains transporting goods from the Port of Baltimore to Philadelphia and markets on the East Coast and in the Midwest. It is part of the CSX Corporation's rail transportation network, and is almost 1.7 miles in length. In November 2021, reconstruction of the Howard Street Tunnel began in order to add an additional 18 inches of vertical clearance that would allow double-stack trains to pass from the Port of Baltimore through Baltimore City. Scheduled to be completed by 2025, this work also will remove obstructions at 21 other locations to allow unrestricted rail passage along the I-95 rail corridor between Baltimore and Philadelphia. When the tunnel project is finished, double-stack trains from Baltimore will be able to go into the Ohio Valley and to Chicago, and the East Coast will have full double-stack rail capacity from Maine to Florida.

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