This assessment of the Office of the Great Barrier Reef in Queensland, Australia established five institutional goals: cohesive staff, credible science, resilient organization, relevance to stakeholders, and effective outreach. Each goal had its own set of indicators.

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The Great Barrier Reef is the largest and best-known coral reef ecosystem in the world. This first report card provides an estimate of the status of the key indicators for the period preceding 2009. It is based on historical data and trends and takes into account the influence of a variable climate from year to year. This serves as a baseline that will be used as a point of comparison to measure progress towards Reef Plan goals and targets.

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This document contains report card summaries for the Cape York, Wet Tropics, Burdekin, Mackay-Whitsunday, Fitzroy, and Burnett-Mary regions. Each section details the region profile, and key findings, as well as summarizing the report card results for land practices, catchment indicators and loads, and the marine parameters; water quality, seagrass, and corals. It also describes positive actions in the regions to improve ecosystem health.

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The Great Barrier Reef World Heritage Area is renowned internationally for its ecological importance and beauty. However, despite it being one of the best managed coral reefs in the world there is a very real risk of damage to the reef from climate change. This technical document details all aspects of the report card process. It includes sections on management, methods, and detailed results for all regions.

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The Mackay-Whitsundays-Isaac region is diverse, with rainforests, ranges, creeks and rivers, wetlands, beaches, islands and reefs which support high biodiversity. The region supports productive agriculture, particularly grazing and sugarcane, as well as expanding urban centres. The Mackay-Whitsundays-Isaac region is rapidly developing due to economic development, climate, livability and natural beauty. This region is expected to double in population within twenty five years.

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The Marine Monitoring Program is a long-term water quality and ecosystem heath monitoring program carried out in the inshore region of the Great Barrier Reef Lagoon. The program is an integral component of the Reef Water Quality Protection Plan, that will help to assess the long-term effectiveness of Reef Plan in reversing decline in the quality of water entering the Great Barrier Reef Marine Park.

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Tissue samples of liver and blubber were salvaged from fifty-three dugong (Dugong dugon) carcasses stranded along the Queensland coast between 1996 and 2000. Liver tissue was analysed for a range of heavy metals and blubber samples were analysed for organochlorine compounds. Metal concentrations were similar in male and female animals and were generally highest in mature animals.

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The abundance and productivity of benthic microalgae in coral reef sediments are poorly known compared with other, more conspicuous (e.g. coral zooxanthellae, macroalgae) primary producers of coral reef habitats.

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While the remote-sensing community attempts to find measures of reef ‘‘health’’ able to be detected and mapped using satellite image data, internationally recognized field assessments are already in place to document benthic cover, among other parameters, as an indicator of coral reef status. Reef Check is one such program, designed in 1996 as a globally applicable, rapid, field-survey protocol for coral reef health monitoring by volunteer divers (Hodgson 1999).

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Coral cays form part of the Australian Great Barrier Reef. Coral cays with high densities of seabirds are areas of extreme nitrogen (N) enrichment with deposition rates of up to 1000 kg N ha(-1) y(-1). The ways in which N sources are utilised by coral cay plants, N is distributed within the cay, and whether or not seabird-derived N moves from cay to surrounding marine environments were investigated.

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