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The Mississippi River Squadron was the Union naval squadron that operated on the western rivers during the American Civil War and was therefore commonly known as the Western Flotilla and sometimes as the Mississippi Flotilla.

The squadron was created on May 16, 1861, and was controlled by the Union Army until September 30, 1862. John Rodgers was the first commander of the squadron and was responsible for the construction and organization of the fleet. Flag Officer Andrew H. Foote relieved Rodgers and encouraged the army commander in the west, Major General Henry W. Halleck, to authorize an expedition down the Tennessee River against Fort Henry. Operating in conjunction with Ulysses S. Grant's army of the District of Cairo (later named the Army of the Tennessee), Foote subdued Fort Henry before Grant's troops could take their positions.

Foote led the squadron in the attack on Fort Donelson and then joined with Maj. Gen. John Pope's Army of the Mississippi for a joint attack on Island No. 10 on the Mississippi River. Charles H. Davis relieved Foote and proceeded to capture Fort Pillow on the Mississippi. The U. S. Ram Fleet commanded by Colonel Charles Ellet, Jr., was added to the squadron during the Battle of Memphis. After the capture of Memphis the squadron was transferred to the control of the U.S. Navy. Davis aided Grant's first and unsuccessful campaign against Vicksburg. Rear Admiral David D. Porter relieved Davis in command and led the squadron at Arkansas Post and during the successful Vicksburg Campaign and siege of the city. Porter led the squadron during the disastrous Red River Campaign and when the waters of the river dropped the fleet was almost lost. The engineering abilities of Colonel Joseph Bailey helped save the fleet. Command temporarily passed to Alexander Pennock before Samuel P. Lee assumed command. Lee was in command until the squadron was discontinued on August 14, 1865.

• Eicher, John H. and Eicher, David J. (2001) Civil War High Commands, Stanford University Press, ISBN 0-8047-3641-3
• Nevin, David (1983) The Road to Shiloh: Early Battles in the West, The Civil War series, Alexandria, VA : Time-Life Books, ISBN 0-80944-716-9

• Mississippi Marine Brigade