• The three Commonwealth Heritage listed sites in the Marine Park owned or managed by the Authority are: 
• Dent Island Lightstation
• Lady Elliot Island Lightstation
• Low Islets Lightstation and Low Island.

Over the past 200 years, lighthouses have played a fundamental role in the settlement and development of Australia.

Safe sea passage was vital for the success of the nation's emerging colonial economy and for a long time the country was entirely dependent on the sea for trade, communication and supplies. Lighthouses were initially built and managed by the respective colonial governments. 

On 1 July 1915, when the Lighthouses Act 1911 came into effect, the Commonwealth officially accepted responsibility for the nation's lighthouses. Management of Commonwealth Islands at this time, including the Great Barrier Reef islands, was the responsibility of AMSA.

In 1988, the Authority increased its involvement in the management of the Commonwealth Islands, eventually taking ownership of the Commonwealth lighthouse islands and their lightstations in 2003. AMSA now leases back any relevant portion of land it uses for Aids to Navigation.

• Dent Island Lightstation
• The lightstation is located on the western side of Dent Island, which is in the Whitsunday region of the Great Barrier Reef, approximately 18 kilometres southeast of Shute Harbour.
• Established in 1879, the lighthouse is important evidence of how navigation aids along the Queensland coast developed and the history of lighthouse technology, accommodation and associated services.
• First lit in 1879, the lighthouse was built in response to the dramatic expansion of regular coastal shipping along the inner route of the Great Barrier Reef following the economic development of northern Queensland.
• The lightstation demonstrates the colonial government’s policy of investing in infrastructure, such as railways and lighthouses, to encourage the expansion of economic activity.
• The land surrounding the lighthouse contains two houses, an engine room, winch house, derrick crane, landing platform, boat platform and access ladder, workshop/store/radio room, tramline, trolley and cables, metal water tank and stand, paths, stairs, graves and fowl house.
• The lightstation complex dating from 1879 to 1960 is a complete intact example of a lightstation complex in Queensland.
• Later stages of development have joined with the original fabric and detail of the lightstation to keep a functioning and effective aid to navigation.
• The Dent Island Lightstation Heritage Register and the Dent Island Lightstation Heritage Management Plan identifies the lightstation’s historical and cultural values and how to protect and conserve these values

• Lady Elliot Island Lightstation
• Lady Elliot Island is at the southernmost end of the Great Barrier Reef. It is a Commonwealth Island managed jointly by the Great Barrier Reef Marine Park Authority and the Queensland Parks and Wildlife Service under a collaborative lease arrangement with a tourism operator. 
• The Lady Elliot Island Lighstation, established in 1866, forms an integral part of history in aiding navigation along the Queensland coast through the Great Barrier Reef.
• The centrepiece is a lighthouse, first lit in 1873, which was only the third lighthouse built by Queensland authorities and was the first constructed offshore within the Great Barrier Reef.
• The Lady Elliot Island Lighthouse was designed using a unique composite form of construction that combined the economy of timber framing with the weatherproof durability of iron plating. 
• The lighthouse was the prototype for this style of lighthouse construction, which was subsequently used elsewhere along the Queensland coast. 
• The Lady Elliot Island Lightstation Heritage Register and the Lady Elliot Island Lightstation Heritage Management Plan describe and assess the heritage values and set out the appropriate management regime for its protection. 

• Low Islets Lightstation and Low Island
• Low Island is a sandy coral cay and one of two small islands that make up the Low Isles in the Great Barrier Reef Marine Park. The other island is Woody Island, an uninhabited coral/mangrove island.
• The islands are located 13 kilometres from Port Douglas and are situated on the western edge of the main shipping channel.
• The Low Islet Lightstation and Low Island has significant heritage value because of the place's importance to Australia's natural and cultural history.
• The place has significant heritage value because of the place's importance as part of the Indigenous tradition, the Kuku Yalanji and Yiriganji Traditional Owner groups visit the site regularly.
• The Low Isles Lightstation and Low Island Heritage Management Plan is due to be finalised in the 2021-22 financial year, with AMSA preparing the lighthouse section.
• As the plan is under development, the Low Isle's cultural and heritage values are currently managed in accordance with the Burra Charter 2013 and the Cairns Area Plan of Management 1998.