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In September 1861, a schooner called the ''William H. Judah'', of which the Confederacy had contracted the use, ran the Union blockade and successfully entered Pensacola's harbor, docking at the navy yard. When it became apparent to Union forces that the Confederacy was attempting to outfit the ''Judah'' as a [[Wikipedia:Privateer|privateer]], they developed a plan to sabotage the work. In the early morning hours of [[September 14]], a Federal raiding party of about 100 sailors and marines in four small boats cast off from the ''[[Wikipedia:USS Colorado (1856)|USS Colorado]]'' bound for the ''Judah''. Approaching the vessel at around 3:30 AM, they were greeted with musket fire from Confederate guards; however, the raiding party successfully boarded the ''Judah'' and set it aflame. The raiding party also managed to spike a gun battery at the navy yard before retreating. The small clash resulted in three deaths apiece on both sides, the first of the war in Florida, as well as several wounded.<ref name="PICW" /><ref>[http://www.flheritage.com/archaeology/projects/shipwrecks/legacy/shipwreck.cfm "U.S. Navy and Confederate Shipwreck Project."] ''Florida Division of Historical Resources''.</ref>

In response to the attack on the ''Judah'', Confederate general Braxton Bragg ordered an attack on [[Fort Pickens]]. A force of over 1,000 men under general [[Wikipedia:Richard H. Anderson|Richard H. Anderson]] set out from Pensacola on the evening of [[October 8]], landing on [[Santa Rosa Island]] about four miles east of Fort Pickens. From there the Confederate troops were divided into three groups: one which travelled on the north (Sound) side of the island, one which travelled on the south (Gulf) side, and a third which trvalled just behind both, used as a flank to connect the groups. After marching for three miles, the Confederate troops were spotted by an encampment of the [[Wikiepdia:6th New York Volunteer Infantry|6th New York Volunteer Infantry]] and fired upon. However, the Confederate troops had the element of surprise and quickly overwhelmed the encampment, sending the 6th New York retreating back to Fort Pickens. Soon after, though, the Confederate general Anderson decided to retreat, during which Union forces pursued and caused extensive casualties. The retreat is described in the ''Florida Historical Quarterly'' article, "Pensacola in the Civil War":

{{cquote|As dawn was rapidly approaching, and the fort and batteries were alerted to his assault, [Anderson] abandoned his plans for any further attack and ordered his troops to march back to their original point of debarkation.