Cedar Keys NWR is managed as part of the North Florida Refuges Complex. A National Wildlife Refuge Complex is an administrative grouping of two or more refuges, wildlife management areas or other refuge conservation areas that are primarily managed from a central office location. Refuges are grouped into a complex structure because they occur in a similar ecological region, such as a watershed or specific habitat type, and have a related purpose and management needs. Typically, a project leader or complex manager oversees the general management of all refuges within the complex and refuge managers are responsible for operations at specific refuges. Supporting staff, composed of administrative, law enforcement, refuge manager, biological, fire, visitor services, and maintenance professionals, are centrally located and support all refuges within the complex.
Other refuges in the Complex are St Marks NWR, Lower Suwannee NWR, Crystal River NWR, and the Tampa Bay Refuges. The Refuge Complex headquarters is located at St Marks NWR, 1255 Lighthouse Rd, St Marks, Fl., 32355.
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The historic Cedar Keys Light Station was established to protect ships that came into Florida's first port.