The Ecosystem Science Management Program supports science-based management by providing resource mapping, modeling, monitoring, research and scientific oversight. The primary focus of this program is to support adaptive management of Rookery Bay National Estuarine Research Reserve's (RBNERR) natural and cultural resources. Using the scientific method to create baseline conditions of aquatic habitats allows for objective analyses of the changes occurring in the state's natural and cultural resources. The Ecosystem Science and Resource Management programs work closely together on many aspects of research, monitoring and management.

RBNERR conducts research through two system-wide efforts - the Graduate Research Fellowship Program and the NERR System's Science Collaborative Program.

Research projects have included:

• Mangrove ecology.
• Oyster reef ecology.
• Crocodile biology.
• Sea turtle biology.
• Shark ecology.
• Food web dynamics.
• Toxicology.
• Mangrove genetics.
• Archaeology.
• Mangrove herbivore interactions.
• Wetland restoration ecology.

• Bacterial genetics.
• Historic salinity patterns.
• Phytoplankton dynamics.
• Sediment accretion rates.
• Terrestrial habitat mapping.
• Freshwater fish physiology.
• Dune habitat ecology.
• Estuarine nutrient cycling.
• Exotic vegetation physiology.