The reserve is managed by the North Carolina Department of Environment and Natural Resources, Division of Coastal Zone Management, as part of the state’s Coastal Reserve Program. The Coastal Reserve has 15 employees located in offices at Kitty Hawk, Columbia, Beaufort and Wilmington. In addition to the four North Carolina Reserve sites, staff also oversees six other coastal natural areas that are managed for the same goals of research, education and compatible public uses.

Given the complexity of the program, various partnerships and committees have been developed to assist in implementation of the North Carolina Reserve management plan. The reserve is affiliated with University of North Carolina at Wilmington, Duke University Marine Laboratory and a wide network of federal, state and local partners. Each component has a 10 to 15 member local advisory committee that provides input for stewardship issues and helps with volunteer projects. The Carolina Estuarine Reserve Foundation, a non-profit friends group for all ten sites, has been created to further the state program mission.