Due to its isolation, the area that is now the refuge was historically used for stock grazing, hunting, and fishing. It was acquired by the Federal Government for an Aviation Experimental Station in 1917. Air Force records indicate that the area was used as a gunnery and bombing practice range until the latter part of the 1950's. On April 24, 1972, the area was transferred to the Department of the Interior. Attempts to clear the military munitions from the property have only been partially successful, largely due to the nature of the fragile wetlands. Disruption of wetland soils cause the soils to become vulnerable to invasive species germination, thus making removal of subsurface ordnances biologically impractical and contrary to the refuge's primary objectives.
In the past, NASA has also used the area as a free flight zone for testing model aircraft. It remains an emergency jettison zone for the Air Force.
In 2003 Eastern Virginia Rivers National Wildlife Refuge Complex began administering the Plum Tree National Wildlife Refuge. Back Bay National Wildlife Refuge in Virginia Beach had previously managed it as an unstaffed satellite.
National priorities such as funding military operations overseas, homeland security, and hurricane relief have resulted in declining federal discretionary funding for the U.S. Fish and Wildlife Service and other Department of the Interior agencies. This decline is expected to continue for the foreseeable future, and the Service must make financial and human resource changes to manage effectively in this situation. Due to declining budgets and increased operating costs, the Service has designated numerous refuges as unstaffed satellite refuges. Three units of the Eastern Virginia Rivers NWR Complex, James River, Plum Tree Island, and Presquile national wildlife refuges, have been designated as unstaffed satellites and are being managed from the Complex headquarters in Warsaw, Virginia.
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The refuge is not open to the public. Due to safety concerns associated with its former use as a bombing range, public access is prohibited. Unauthorized entry is a federal offense and is punishable by fine and possibly imprisonment.