Green Cove Springs is a city in Clay County, Florida, United States. The population was 5,378 at the 2000 census. As of 2004, the population recorded by the U.S. Census Bureau is 5,990 . It is the county seat of Clay County. The city is named after the portion of the St. Johns River upon which the city is built. The river bends here, and the area is sheltered by trees that are perennially green.