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. Channelization, inter basin diversion, and other flood control projects had significantly altered the habitat of the sparrow over the years and its numbers declined since its discovery 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. 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.