The area was first inhabited over 7,000 years ago by Native Americans attracted to a warm mineral spring.

Today, the sulfur-scented spring water feeds an adjacent public swimming pool before flowing the short distance to the St. Johns River.

Agriculture and tourism were the two primary economic activities in the area until the end of the 19th century, when Henry Flagler's railroad began taking tourists further south in Florida.

The Village Improvement Association led local efforts to beautify the town, and established its first public library.

[5][6] The period immediately before and during World War II again brought new growth to Green Cove Springs.

In August 1943, the facility was renamed Naval Air Station Green Cove Springs and consisted of four 5,000-foot (1,500 m) asphalt runways.

[10][11] Though the original air traffic control tower is still standing, attached to one of the former Navy aircraft hangars, the airfield remains an uncontrolled facility.

Locally, the community is known as the home of Gustafson's Farm, a brand name of milk and dairy products sold throughout Florida.

Gustafson's has many bottling plants across the state, stretching from Tallahassee in the west to Tampa and Cocoa in the south.

The department currently consists of 29 sworn officers, part-time and full-time dispatchers, an evidence custodian, an administrative secretary, and two crossing guards.

The department makes use of mobile data terminals in all of their patrol vehicles for reporting and obtaining information on the streets.

In April 2014, the agency moved into a newly built police station and emergency operations center at 1001 Idlewild Avenue.

The city of Green Cove Springs contracts with the Clay County Fire-Rescue Department for fire and medical services.

The Hibernia post office was reestablished on February 16, 1855, and remained open until May 15, 1931, when it was closed and the area assigned to Green Cove Springs.

[14] Green Cove Springs is located on the eastern border of Clay County at 29°59′34″N 81°41′2″W / 29.99278°N 81.68389°W / 29.99278; -81.68389 (29.992716, –81.683786),[15] along the St. Johns River.

State Road 16 departs west from the center of the city and leads 27 miles (43 km) to Starke.

SR 16 leaves eastbound from US 17 south of the city center and crosses the St. Johns River by the Shands Bridge, leading to St. Augustine 25 miles (40 km) to the east.

By the late 2020s, the First Coast Expressway, a major toll bypass road connecting I-10 and I-95, is expected to pass to the west and south of Green Cove Springs.

Sacred Heart Catholic Church, part of the Diocese of St. Augustine, was founded as a mission back in 1874, and now serves the city.