The Great Barrier Reef Marine Park Authority was recognised with the following regional, national and international awards.

• 2010 October, World Future Council's Silver Future Policy Award for the Australian Government's efforts to protect the Great Barrier Reef in particular the statutory Zoning Plan based on the Representative Areas Program
• 2009 October 'Best Practice in Federal Government Excellence Awards' in the 2009 Public Sector Excellence Awards of Public Administration (IPAA)- Queensland for the development of the Great Barrier Outlook Report 2009
  
• 2009 October Environment Institute of Australia and New Zealand (EIANZ) Award for Excellence in Professional Practice 2009 (4 elements – Outlook Report, Climate Change, Environmental Assessment and Management and Reef Guardian Schools)
  
• 2009 April 'Top 25' Ecological Restoration Projects in Australasia selected by the Global Restoration Network (GRN)
• 2007 November Public Sector Management Award in the 2007 Tourism and Transport Forum (TTF) Corporate Leadership Awards
• 2007 June  Excellence in Marine and Coastal Management Award at the United Nations Association of Australia World Environment Day Awards 2007
• 2007 May  World Travel and Tourism Council’s Tourism for Tomorrow Destination Award
  
• 2006 August  Australian Government Minister's Achievement Award
  
• 2005 October  World Wide Fund for Nature (WWF) Gift to the Earth
• 2005 July  Sultan Qaboos Prize for Environmental Preservation for UNESCO's Man and the Biosphere Programme, jointly to the Great Barrier Reef Marine Park Authority and Dr Ernesto C. Enkerlin-Hoeflich (Mexico)
• 2005 April  Planning Institute of Australia, National Awards
  • National Award for Community Based Planning,
  • Planning Minister’s Award, Overall National Award for Excellence in Planning
• 2004 December  US Coral Reef Task Force Award for Outstanding Management (International)
• 2004 November  Planning Institute of Australia, Queensland Division
  • Award for Environmental Planning/Conservation
  • Award for Community Based Planning
  • Overall Winner for Excellence in Planning
• 2004 August  Eureka Prize for Biodiversity Research
• 2004 August  ESRI International User Conference Award (Special Achievements in Geographical Informational Systems)
• 2004 June Banksia Environmental Award(for Government Leading by Example for a Sustainable Future)