US Navy Base at Mayport Mills, Florida, St. Johns River (Fla. Dept. of State on-line photo archive):
After taking Ft. Clinch and the Town of Fernandina on 3-4 March 1862, elements of the South Atlantic Blockading Squadron, along with transports carrying US Army troops, arrived off the mouth of the St. Johns River, Florida on 8 March 1862. After reconnoitering the bar at the river mouth, and after repeated attempts to cross, Lt. Thomas H. Stevens of the gunboat USS Ottawa took the ship’s helm himself, ordered “full speed ahead,” and scraped across the bar on 11 March, along with the gunboats Seneca, Pembina, and Ellen. Ottawa, Seneca, and Pembina were all “Unadilla” class (“90-day”) gunboats, and Ellen was a converted New York ferryboat. Lighter draft ships had penetrated upriver prior to that and captured Ft. Steele, a small Confederate fortification near the mouth of the river built of palmetto logs and armed with 7 guns. The Confederates had abandoned the fort a few days earlier after sighting the arrival of the Union flotilla off the river mouth.
On 12 March, the first occupation of the City of Jacksonville occurred, as companies of the 4rth New Hampshire Infantry Regiment were landed. Jacksonville had a fairly large proportion of pro-Union folks, who were overjoyed to see the Union occupation of the city. To their dismay and horror, by the end of the month, Army forces were ordered withdrawn from the city. Officers on the Union Navy vessels were aghast at this action. In an effort to provide some assistance, the Navy established a permanent base of operations at Mayport Mills, three miles upstream of the river mouth and about 6-7 miles downstream of Jacksonville.
On 10 March 1862, the USS Wabash hove to off the mouth of St. Augustine Inlet, south of the St. Johns River mouth. Shallow depths in the inlet and the harbor did not allow the huge Wabash to enter, and heavy weather that day restricted the use of ship's boats to cross the bar in the Inlet. The next day, 11 March, Commander C.R.P. Rogers entered the inlet in a ship's boat with an unarmed landing party, arrived at the harbor, and accepted the surrender of Ft. Marion (the present-day Castillo de San Marcos National Monument) and the adjacent Town of St. Augustine, Florida. In the span of barely two weeks, the Union Navy and Army had secured a strong foothold in a big chunk of northeast Florida, securing fortifications, land, and secure harbors. This formed the basis for subsequent operations in this area of Florida.
Fort Marion, St. Augustine (Fla. Dept. of State on-line photo archive):