The Mississippi River Squadron was the Union brown-water naval squadron that operated on the western rivers during the American Civil War. It was initially created as a part of the Union Army, although it was commanded by naval officers, and was then known as the Western Gunboat Flotilla and sometimes as the Mississippi Flotilla. It received its final designation when it was transferred to the Union Navy at the beginning of October 1862.

The Union Navy was the United States Navy (USN) during the American Civil War, when it fought the Confederate States Navy (CSN). The term is sometimes used carelessly to include vessels of war used on the rivers of the interior while they were under the control of the United States Army, also called the Union Army.