- Between September 16, 2004 and August 29, 2005 Hurricanes Ivan, Dennis, Cindy and Katrina plus Tropical Storm Arlene hit Gulf Islands National Seashore.
- Although most areas have reopened as a result of recovery efforts, two major roads in the Florida District remain closed, Fort Pickens Road and J. Earle Bowden Way (State Road 399).
- The Santa Rosa Area remains closed. All facilities were damaged by tropical storms and hurricanes in 2004 and 2005.
- The Fort Pickens Campground in the Florida District and the Davis Bayou Campground in the Mississippi District remain closed. The Davis Bayou Campground is being used by the Federal Emergency Management Administration (FEMA) for displaced homeowners.
- The Seashore's submerged and terrestrial cultural resources, archeological sites, forts, and structures, have not been comprehensively surveyed or evaluated. The eroding effect of natural processes and human activities creates a constant challenge for protecting, preserving , and interpreting these windows to the past.
- The Seashore encompasses barrier islands and estuaries that provide habitat for a variety of species including approximately 25 endangered or threatened species. This habitat is influenced by water quality degradation, alternating water flow, the introduction and spread of exotic, invasive and nuisance species, and increasing recreational uses such as boating.
- Population growth along coastal regions in Florida, Alabama, and Mississippi is increasing pressure on the Seashore to accommodate local recreational demands. Balancing high-quality visitor experience while protecting resources is difficult.
- There is a need to upgrade and improve the Seashore's interpretive efforts to educate visitors on the natural and cultural resources within the ecosystem that encompasses the Gulf Coasts of Florida and Mississippi.
- The Seashore has acquired approximately half of the 2,200-acre Cat Island in Mississippi. Numerous issues relating to limits/impacts of visitation, development of facilities, protection of cultural and natural resources and interpretation need to be resolved.