On 13 August 2004, the first of four hurricanes to strike Florida in 50% and sometimes 90% of their vegetation severely damaged (dead, broken tree stems, and tipped trees). Shell Mound Trail of JNDDNWR sustained catastrophic damage to its old growth mangrove forests. Direct storm mortality and injury to manatees in the area was probably slight. Because seagrass beads and manatee habitat extend beyond refuge boundaries, we recommended a regional approach with partner agencies to more thoroughly assess storm impacts and monitor recovery of seagrass and manatees. Besides intensive monitoring of waterbirds and their nesting habitat (pre- and post-storm), we recommend that the Mangrove Cuckoo be used as an indicator species for recovery of mangrove forests and also for monitoring songbirds at risk. Black-whiskered Vireo may be another potential indicator species to monitor in mangrove forests. Damaged vegetation should be monitored for recovery (permanent or long-term plots), especially where previous study plots have been established and with additional plots in mangrove forests of waterbird nesting islands and freshwater wetlands. Potential loss of wetlands may be prevented by water level monitoring, locating the positions (GPS-GIS) and maintaining existing water control structures, creating a GIS map of refuge with accurate vertical data, and monitoring and eradicating invasive plants. Invasive species, including Brazilian pepper (Schinus terebinthifolius) and air potato (Dioscorea bulbifora), were common in a very limited survey. As an important monitoring goal, we recommend that species presence-absence data analysis (with probability of detection) be used to determine changes in animal communities. This could be accomplished possibly with comparison to other storm-damaged and undamaged refuges in the Region. This information may be helpful to refuge managers when storms return in the future.