On September 18, 2003, Isabel blew down many trees, making most of the refuge's 100-mile road system impassable. Its high winds damaged roofs, water control structures, kiosks and boardwalk trails. It collapsed the upper portion of the radio communications tower and destroyed 3,000 acres of mature Atlantic white cedar forest. With the blown-down timber came an increased potential for major wildfires within the next 3-5 years.

Nevertheless, considerable progress has been made in restoring refuge operations and habitat:

• Funds were allocated by the Northeast Regional Office to remove damaged trees, restoring 30 miles of road. Contracts to clear the roadwaysended in early September 2004, when funds were exhausted. Refuge personnel had already cleared about 60 miles of road during the months immediately after the hurricane, and about 10 miles of road now remain to be cleared.
• Radio communications were restored on the partially collapsed communications tower, but radio coverage has been reduced. Agency radio technicians are currently negotiating with a local public television station to install new transmission equipment on its broadcasting tower in northern Suffolk.
• Volunteers partially repaired the Dismal Town Boardwalk Trail to allow reasonably safe use by refuge visitors, however, the entire boardwalk system will need to be rebuilt in coming years before it will be fully usable.
• The refuge is working with the Northeast Region's Division of Contracting and General Services to contract for roof replacement work on several buildings.
• A permit was issued to salvage about 100 acres of storm-damaged Atlantic white cedar, a globally-rare tree species. About 60 acres of cedar were harvested by the end of September 2004.
• In August, managers conducted the public review of helicopter-supported salvage and restoration of damaged Atlantic white cedar forests.