In 1861, Confederate battery positions on Jekyll Island were equipped with one 42-pounder gun and four 32-pounder navy guns en barbette, each having about 60 rounds of shot and shell. Casemates, hot shot furnace and magazines are recorded, also. Of greater strength than batteries on St. Simons Island, the earthworks of palmetto logs, heavy timber, sandbags, and railroad irons were mounted for the protection of Brunswick.
February 10, 1862, Gen. Robert E. Lee requested permission from Gov. Joseph E. Brown to dismantle the stronghold as "the inhabitants of the island and Brunswick have removed themselves and property" to inland points. Maj. Edward C. Anderson removed the guns, sending them to Savannah.
March 9, 1862, Lt. Miller of the USS Mohican landed a rifle company and marines, hoisting the Union flag over the island.
In January, 1863, to strengthen fortifications at Port Royal, S.C., a Federal force was sent by flatboat to seize the railroad irons. Some of the men who had helped build the defenses guided the detachment to them and "the men enjoyed demolishing them far more than they had relished their construction."