High ground along the river and a flowing mineral spring drew the first inhabitants to this area some 7000 years ago, but historic development dates from 1816 when George I. F. Clarke erected a sawmill in this vicinity under a Spanish land grant. The first settlement, called White Sulfur Springs, was established in 1854, with a wharf, a store, and several houses clustered around a public square. During the Civil War, Federal troops frequently skirmished with Confederate forces in the vicinity, and finally occupied the town in 1864. Renamed in 1866, Green Cove Springs became the seat of Clay County government in 1871. Tourism flourished, surpassing citrus culture and lumbering as the area's economic base. River steamers brought visitors to the "Saratoga of the South", noted for the healthful qualities of its famous spring and for hotels and boarding houses said to rival the finest to be found in northern resorts. By the 1890s, the population reached more than 1500. But an expanding railroad system carried tourists southward and a great freeze in 1895 destroyed the surrounding citrus groves. The city's tourist industry declined sharply.
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The advent of the automobile age and the creation of a state highway system provided the basis for economic recovery in the 1920s, when the city shared in the general prosperity of the Florida Land Boom. But the collapse of the boom and the depression of the 1930s marked the end of the early development of the city. Between 1940 and 1945, the city experienced renewed development. The population increased from 1752 to 3026 as a result of the wartime construction of Benjamin Lee Field, a 1500 acre air auxiliary complex, by the U. S. Navy. With the end of World War II, thirteen piers were constructed by the Navy and the Green Cove base became home port to a "mothball fleet" of some 600 ships. With its share of returning war veterans, the community's population grew through the 1950s to a total of 4233 in 1960. In 1961, the Navy decommissioned its base and the reserve fleet was transferred to another facility. In 1984, the city annexed the former naval base into its corporate limits, tying this part of its heritage to its future growth and development.