Each year the refuge treats hundreds of acres of invasive exotic Brazilian Pepper and Australian pine trees which displace native plants. The objective of this chemical and manual management activity is to protect and enhance the native subtropical habitats for indigenous flora and fauna. Prescribed fires, controlled fires intentionally set by managers, are used to manage and enhance native subtropical habitats by mimicking historical natural fire events that functioned to maintain native plant communities. Prescribed fires reduce midstory and overstory vegetation on ridges, maintain early successional species, and help control young exotic plants. Prescribed burning reduces hazardous accumulations of flammable fuels and kills invasive woody vegetation.

Regular wildlife surveys are conducted to monitor populations of migratory birds and their production, and to establish trends for a number of species, primarily birds. The refuge monitors colonial nesting and roostingbird numbers, shorebird populations, mottled duck, pelican and osprey production, and alligator and red-shouldered hawk abundance. A weekly Wildlife Drive survey is conducted on Fridays to monitor the abundance and diversity of bird populations using refuge wetlands. Water levels are monitored continuously.