After the Union victory in the Battle of Mobile Bay, Mobile nevertheless remained in Confederate hands. Spanish Fort was heavily fortified as an eastern defense to the city of Mobile. Fort Huger, Fort (Battery) Tracey, Fort (Battery) McDermott, Fort Alexis, Red Fort, and Old Spanish Fort were all part of the Mobile defenses at Spanish Fort.
Union forces embarked on a land campaign in early 1865 to take Mobile from the east. Maj. Gen. E.R.S. Canby's XIII and XVI corps crossed the Fish River at Marlow Ferry, and moved along the eastern shore of Mobile Bay forcing the Confederates back into their defenses. Union forces then concentrated on Spanish Fort and Fort Blakely, five miles to the north. On March 27, 1865, Canby’s forces rendezvoused at Danley's Ferry and immediately undertook a siege of Spanish Fort. The Union had enveloped the fort by April 1, and on April 8 captured it. Most of the Confederate forces, under the command of Brig. Gen. Randall L. Gibson, escaped and fled to Mobile, but Spanish Fort was no longer a threat.
With Spanish Fort's fall on April 8 and Gen. Robert E. Lee's surrender at Appomattox Court House the next day (unrelated to the fall of Spanish Fort, as Lee’s forces were in Virginia), Fort Blakely remained the last organized resistance to the Union east of the Mississippi River. However, as early as April 1, when Spanish Fort's fall became inevitable, Union forces had begun moving north in order to concentrate on Fort Blakely, which eventually succumbed late on April 9 in the Battle of Fort Blakely.
The falls of Spanish Fort and Fort Blakely permitted Union troops to subsequently enter Mobile unopposed after the conclusion of the Civil War, occupying it on April 12, 1865.