In early 1861 the critical border state of Kentucky had declared neutrality in the American Civil War. This neutrality was first violated on September 3, when Confederate Brig. Gen. Gideon J. Pillow, acting on orders from Maj. Gen. Leonidas Polk, occupied Columbus, Kentucky. The riverside town was situated on 180 foot high bluffs that commanded the river at that point, where the Confederates installed 140 large guns, underwater mines and a heavy chain that stretched a mile across the Mississippi River to Belmont, while occupying the town with 17,000 Confederate troops, thus cutting off northern commerce to the south and beyond.
Two days later, Union Brig. Gen. Ulysses S. Grant, displaying the personal initiative that would characterize his later career, seized Paducah, Kentucky, a major transportation hub of rail and port facilities at the mouth of the Tennessee River. Henceforth, neither adversary respected Kentucky's proclaimed neutrality, and the Confederate advantage was lost. The buffer zone that Kentucky provided between the North and the South was no longer available to assist in the defense of Tennessee.
By early 1862, a single general, Albert Sidney Johnston, commanded all the Confederate forces from Arkansas to the Cumberland Gap, but his forces were spread too thinly over a wide defensive line. Johnston's left flank was Polk, in Columbus with 12,000 men; his right flank was Brig. Gen. Simon Bolivar Buckner, in Bowling Green, Kentucky, with 4,000 men; the center consisted of two forts, Forts Henry and Donelson, under the command of Brig. Gen. Lloyd Tilghman, also with 4,000 men. Forts Henry and Donelson were the sole positions defending the important Tennessee and Cumberland Rivers, respectively. If these rivers were opened to Union military traffic, two direct invasion paths would lead into Tennessee and beyond.
The Union military command in the West suffered from a lack of unified command, and were organized into three separate departments: the Department of Kansas, under Maj. Gen. David Hunter; the Department of Missouri, under Maj. Gen. Henry W. Halleck; and the Department of the Ohio, under Brig. Gen. Don Carlos Buell. By January 1862, the disunity was apparent because they could not agree on a strategy for operations in the Western Theater. Buell, under political pressure to invade and hold pro-Union eastern Tennessee, moved slowly in the direction of Nashville. In Halleck's department, Grant moved up the Tennessee River to divert attention from Buell's intended advance, which did not occur. Halleck and the other generals in the West were coming under political pressure from President Abraham Lincoln to participate in a general offensive by Washington's birthday (February 22). Despite his tradition of caution, Halleck eventually reacted positively to Grant's proposal to move against Fort Henry. Halleck hoped that this would improve his standing in relation to his rival, Buell. Halleck and Grant were also concerned about rumors that Confederate General P.G.T. Beauregard would soon arrive with 15 Confederate regiments. On January 30, 1862, Halleck authorized Grant to take Fort Henry.
Grant wasted no time, leaving Cairo, Illinois, at the confluence of the Mississippi and Ohio Rivers, on February 2. His invasion force, which arrived on the Tennessee River on February 4 and 5, consisted of 15–17,000 men in two divisions, commanded by Brig. Gens. John A. McClernand and Charles F. Smith, and the Western Gunboat Flotilla, commanded by United States Navy Flag Officer Andrew Hull Foote. The flotilla included four ironclad gunboats (flagship USS Cincinnati, USS Carondelet, USS St. Louis, and USS Essex) under Foote's direct command, and three timberclad (wooden) gunboats (USS Conestoga, USS Tyler, and USS Lexington) under Lt. Seth Ledyard Phelps. Insufficient transport ships this early in the war to deliver all of the army troops in a single operation required two trips upriver to reach the fort.