St. Johns National Wildlife Refuge (SJNWR) was established in 1971 to protect the dusky seaside sparrow. In 1990, the species was officially declared extinct and the critical habitat was delisted. Today, SJNWR is managed to provide habitat for several species of birds listed as species of special management concern by the U.S. Fish and Wildlife Service and for wildlife and habitat diversity, primarily by prescribed fire. A marsh restoration project was conducted on the Highway 50 Unit in 1990 to return sheetflow from the St. Johns River. Dike roads traversing the Refuge in an east-west fashion were removed and clumps of spartina were planted.

The initial objective of the refuge was to provide habitat protection for the endangered dusky seaside sparrow, which was declared extinct in 1990. Today, the refuge is managed primarily through controlling burning to maintain habitat for many species classified as threatened, endangered and species of special concern. The marsh savannah present is dominated by cordgrass, black-needle rush, gulf muhly and saw grass. The refuge provides habitat for the endangered wood stork and threatened bald eagles, indigo snakes, American alligator and crested caracara. Waterfowl use is limited to blue-winged teal and ring-necked ducks. However, the refuge received moderate use from greater and lesser yellowlegs, blacknecked stilts and killdeer. Turkey and black vultures frequent the area, as well as occasional hawks. Assorted rabbits, raccoons and rodents can also be found.

The refuge also received usage from the very secretive rails. A black rail research project conducted from 1993-1997 indicated that the refuge has a healthy population of this secretive species. Other rails have been observed on the refuge as well, such as the king and virginia rails.

Due to the sensitive wildlife and habitat in the area, the refuge has been closed to public access.

The St. Johns River was once a vast relic salt marsh system with a high water table that served as a natural drainage system for central Florida. During the early 1900's, however, dikes were constructed and canals dug to provide land for the people beginning to flock to Florida for its warm winters and white beaches. The natural flow of the river, which runs north, began to change as water was redirected, canalized and controlled. Agencies began to realize the impact this management was having on the marsh, and in 1986, the Emergency Wetlands Resources Act was passed that specifically identified the St. Johns River basin as priority for protection.

St. Johns National Wildlife Refuge was established in 1971 for the protection and habitat conservation of an endangered marsh bird called the dusky seaside sparrow, which was discovered in 1872. A total of 6,176 critical acres were acquired to provide adequate habitat to recover the dusky seaside sparrow. Management techniques were immediately initiated and included population surveys on and off the refuge, water level monitoring, fire management investigations, ecological monitoring and habitat manipulations. The immense effort, however, was too late, and the last dusky seaside sparrow in the wild was observed in 1980. The dusky seaside sparrow was declared extinct and its critical habitat delisted in 1990. Today, the refuge remains a significant area for preserving biodiversity, as demonstrated by the variety of threatened, endangered and species of special concern that are present. Prescribed burning is the primary management tool for the refuge, which serves to maintain the natural habitat. Several habitats, such as floodplain marsh, floodplain swamp and scrub found at the refuge are classified as imperiled statewide.