The preserve protects sensitive marine habitats and includes one of the county's largest undeveloped barrier islands as well as numerous mangrove islands and expansive seagrass beds.
Shell Key has been designated as one of the state's most important areas for shorebird nesting and wintering and it serves as an important study area for these species. It also is an important area for recreation. A balance for both uses was established by restricting public use to the northern and southern ends of the island. A central core area for conservation is closed to the public.
Boating, camping, and beach-going activities are permitted in public use areas of the preserve. Visitors can access Shell Key only via a water vessel and no restroom facilities are provided. The closest boat ramps, trailer parking, and restroom facilities are located at nearby at Fort De Soto Park.