By the time of the Civil War, Apalachicola was Florida's largest cotton port and the third largest cotton port on the entire Gulf of Mexico coast behind only New Orleans and Mobile. An active area for blockade running, Union naval vessels of the Gulf Coast Blockading Squadron began closing off the city in June 1861, and most seaborne commerce was effectively halted during the war.

Throughout the war, the Apalachicola vicinity was also an active area for Confederate salt production. As Confederate forces in the area were sent to other locations in early 1862 and the city was left almost defenseless, most of the population fled inland, many of them to Ricco's Bluff some 90 miles up the Apalachicola River.

In April 1862, a small detachment of Union sailors and marines from the USS Sagamore and the USS Mercedita landed at Apalachicola, but withdrew back to their ships after one night.

Although never occupied permanently, Union forces periodically returned to the mostly abandoned city during the remainder of the war.

Information Provided by the Florida Department of State.