Sailors have been flocking to the area surrounding the present site of Naval Station Mayport for more than 400 years. With its ease of access to inland waterways and the open ocean, early Sailors' interest in the region has resulted in an important military base with strong ties to the community.

In 1562, French Huguenot Commodore Jean Ribault, then said to be the greatest captain on the seas, was selected by the famous Admiral Gaspard de Coligny to lead an expedition to Florida; his mission was to form a French Protestant colony. Ribault arrived off what is now known as Mayport, near the mouth of the St. John's River, on May 1 of that year. Landing on the north side of the river, now Ft. George, it is said they offered up prayers while the Native Americans looked on with attentive silence. They were received warmly by the Native Americans, including Satourbia, their chief.

The following morning, on May 2, Ribault entered to the south side of the river with his captains, gentlemen, soldiers and others. They had with them a stone monument which they placed, according to Ribault's narrative, on a sand hill on the south side of the river near its mouth and plainly visible from the sea. In 1564, de Coligny dispatched another French Huguenot, Commodore RenGoulaine de Laudonniere, to establish a colony near the mouth of the St. Johns River. The Spanish were fearful of French domination in north Florida. Their "treasure fleet" followed the gulf stream up the coast of Florida, past the mouth of the St. John's River, and discovered the French positions in the area before crossing the Atlantic Ocean for Spain. With the arrival of this news in Spain, the government dispatched a fleet under command of Pedro de Menendez to the Mayport area to prevent continued French occupation.

At about the same time the Spanish Fleet set sail for this area, reinforcements commanded by Jean Ribault were sent by de Coligny to the French colony. The two fleets, French and Spanish, met near the site of this base, but the Spanish retired to St. Augustine. Soon afterward, the French fleet followed to drive the Spanish away; but, as the French fleet was ready to attack, the ships were swept to the south and wrecked by a violent hurricane.Menendez took advantage of the situation and moved overland to destroy the then defenseless French colony (Ft. Caroline) at St. Johns Bluff. After seizing this area for Spain, and executing the French prisoners, Menendez set up small military outposts: one at the present site of Naval Station Mayport, one immediately across the river, and one at the fort at St. Johns Bluff.

A French expedition under the command of De Gourgues set sail to take revenge for this act. In 1568 De Gourgues entered the St. Johns River and seized the Spanish blockhouse at Mayport, as well as the other two outposts in this area. In reprisal, he executed all the Spanish and then left for France. In 1580, on the river near the base, the Spanish destroyed a French warship. Six years later the English fleet under Sir Francis Drake attempted to land here after attacking St. Augustine, but was prevented by high winds. Through old maps, there is evidence of continuous occupation of the naval station site by Native Americans, Spanish, English, and Americans since the 16th Century. The Native Americans in this area were wiped out by slave traders from South Carolina under Governor Moore in the early 18th Century.

During the Revolutionary War period, Florida was occupied by the English. The river was patrolled by a group of British vessels called the St. Johns Fleet whose duty was to prevent American sympathizers from crossing the river from the south side to the north. During this time many Spanish citizens moved into the Mayport area from the New Smyrna colony. Many of their descendants still live in the City of Mayport, adjacent to the naval station.

At the outbreak of the American Civil War, a Confederate company from Jacksonville, the Jacksonville Light Infantry, set up a fort on the present naval station. They named it Fort Steele in honor of their commanding officer, a medical officer named Dr. Steele. Steele was soon transferred to the Confederate Medical Corps and command of the company was assumed by Captain Doggett. Because the fort was considered indefensible, the guns were buried and the Jacksonville Company was made part of the main Confederate forces in Tennessee. A number of years before the Navy acquired this site; these guns were discovered near the present pilothouse and were recovered.

During the late 19th Century the site of this base was a fashionable resort area.At that time there were no jetties and the wooded area of the base, fronted by a beach, was a shore of the south channel of the St. Johns River. Summer visitors from Jacksonville had their cottages on the area of the base rather than at the beach. In the early 20th century, the site was acquired by a family of northern visitors who established their residences here and set up a group of cottages for rental.

In 1890, there was a flourishing little colony where most of the installations of the Naval Station are now located. There was a red brick lighthouse, the foundation of which was plainly visible about 100 feet out surrounded by three feet of water to a 1,000-foot pier at Wonderwood. There was another large brick home built on the beach, however, a tremendous high tide accompanied by a strong northeast wind swept it and the lighthouse away. In 1932, Sidney Hartley's general store was located where the Security Office is now. Texaco gas was sold here at 21 cents a gallon.

Under the Hepburn Act of May 17, 1938 (Public Law 528 of the 75th Congress) the Honorable Claude Swanson appointed a board to be headed by Rear Adm. A. J. Helpburn to investigate "a southeastern naval air base." In communication to Congress on Dec. 27, 1938, "the board recommends the establishment of a major base at Jacksonville having the following characteristics:
• Facilities for two carrier groups (planned with a view to expansion to four carrier groups)
• Facilities for three patrol squadrons (planned with a view to accommodate six squadrons)
• Facilities for two utility squadrons
• Facilities for complete-plane and engine overhaul
• Berthing for carriers at inner end of entrance jetty
• A channel to permit tender berthing at piers at Camp Foster
• Development of an outlying patrol plane operating area in the lower "Banana River"

The citizens of Duval County (Jacksonville) promised the Navy Department they would buy the 1and for the main Naval Air Base and Carrier Berthing (Naval Station Mayport). Upon passage of H.R. 2880, 76th Congress, 1st Session, which authorized the projects contained in House Document 65, the citizens of Duval County on July 18, 1939 passed a $1,100,000 bond issue to purchase land for the two stations.

In April 1939, the Navy Department initiated plans for this area which included a site along the south jetties for the development of an aircraft carrier basin. In December of that year, on the basis of a report made by Commander Carl Cotter, officer-in-charge of construction, Ribault Bay was selected as the location for such a basin. The basin was dredged to 29 feet and used by patrol craft, target and rescue boats and jeep carriers during World War II. At war's end, $780,000 had been appropriated to build a carrier pier on the north side of the basin. This appropriation, with many others, was cancelled and no improvements were made. On the basis of a proposal submitted by Lieutenant Commander M. R. Sanders, commanding officer, Section Base One, Naval Reserve Armory, recommending establishment of a second section base at Mayport, the station was commissioned as a U.S. Naval Section Base in December 1942.

On April 1, 1944, the air facility at Mayport was commissioned a Naval Auxiliary Air Station (NAAS), commanded by Sanders. At the same time, the Sea Frontier Base was maintained in the bay area. The next year, the Naval Auxiliary Air Station took over the entire site including the pier and docking facilities. During World War II, the U.S. Naval Section Base and Naval Auxiliary Air Station provided vital support to the country's war effort in terms of personnel and logistics. Following the war, both the Naval Section Base and NAAS were de-commissioned and placed in a caretaker status. The Coast Guard took over the base and operated a small "Boot Camp" there for several years, but they vacated Mayport in late 1947 due to budget cuts.

Mayport was reactivated again in June 1948 as a Naval Outlying Landing Field under the cognizance of the Commanding Officer, Naval Air Station, Jacksonville. Three years later the land area of Navy Mayport facilities was increased to 1,680 acres and work began on extending the runway. Through the late 1940's and mid-1950's, the Mayport base continued to grow to accommodate new classes of ships and extended runways for the increasing air traffic.