Great Barrier Reef islands with lighthouses played a fundamental role in the nation's development. Safe sea passage was vital for Australia's emerging colonial economy entirely dependent on the sea for trade, communication and supplies.

Lighthouses were initially built and managed by the respective colonial governments. The need for a national approach to marine navigation policy was apparent, particularly when navigation lighting was required in parts of the colony with comparatively low population numbers, and consequently insufficient funds for appropriate navigation aids.

On 1 July 1915, when the Lighthouses Act 1911 came into effect, the Commonwealth officially accepted responsibility for the nation's lighthouses.

Prior to 1988, management of the Commonwealth Islands was the responsibility of the Australian Maritime Safety Authority (AMSA).

In 1988, the Great Barrier Reef Marine Park Authority (GBRMPA) increased involvement in the management of the Commonwealth Islands, eventually taking ownership of the lighthouse islands in 2003. AMSA now lease back from the Great Barrier Reef Marine Park Authority the relevant portion of land it uses for navigational aids.

Private lease arrangements are in place over some islands, usually either for tourism related purposes such as Lady Elliot Island, or research field work such as with the University of Queensland on Low Isles.

The Great Barrier Reef Marine Park Authority works in partnerships with lessees and other stakeholders for the long-term conservation of these islands.