The Reef Rescue Marine Monitoring Program monitors the condition of water quality and the health of key marine ecosystems such as coral reefs and seagrass in the inshore Great Barrier Reef lagoon.

The Reef Water Quality Protection Plan (Reef Plan) is a joint commitment of the Australian and Queensland Governments that was updated in 2009 through the Australian Government’s $200 million Reef Rescue package as part of its Caring for our Country initiative.

The Marine Monitoring Program is a key component in the assessment of long-term improvements in inshore water quality and marine ecosystem health that are expected to occur with the adoption of improved land management practices in the Reef catchments under Reef Plan and Reef Rescue.

Data from the Marine Monitoring Program is combined with data collected at the paddock and catchment scales. This produces an annual report card summary of the health of the Reef and its catchments as part of the Queensland Government's Paddock to Reef Program.

The monitoring program has four main components and is a collaborative effort between the government, community, scientists and managers. The Great Barrier Reef Marine Park Authority is responsible for the management of the program, in partnership with five monitoring providers:

• Australian Institute of Marine Science
• University of Queensland
• James Cook University
• Queensland Department of Agriculture, Fisheries and Forestry 
• CSIRO
  

Inshore marine water quality monitoring

Water quality monitoring is carried out by measuring the concentrations of nutrients, sediment and pesticides using a variety of techniques, including traditional water sampling methods, satellite remote sensing technologies and state-of-the-art sensors with long-term data logging capacity.

Monitoring the inshore waters of the Reef is required to evaluate the effectiveness of Reef Plan and Reef Rescue in improving the quality of water entering the Reef lagoon from adjacent catchments.

In carrying out the monitoring program, the Australian Institute of Marine Science (AIMS) assesses temporal and spatial trends in marine water quality in inshore areas of the Reef lagoon, while James Cook University monitors water quality during flood events to quantify the exposure of reef ecosystems to land-based pollutants.

The GBRMPA recognises it is important to assess water quality during wet and dry seasons, as a very large proportion of the annual pollutant load is transported to the Reef during floods.

Intertidal seagrass monitoring

Monitoring of seagrass meadows is carried out between Hervey Bay and Cooktown to ensure that any changes in the status of seagrass meadows that are linked to changes in water quality are identified.

The Queensland Department of Agriculture, Fisheries and Forestry and James Cook University measure seagrass abundance, species composition and reproductive status.

Inshore coral reef monitoring

Monitoring of coral reefs is focussed on inshore reefs between the Keppel Islands in the southern Great Barrier Reef and Snapper Island to the north of Cairns. The monitoring ensures that any changes in the status of coral reefs that are linked to changes in water quality are identified.

The Australian Institute of Marine Science carries out the monitoring using video records of the cover of corals and other benthic (bottom-dwelling) organisms, and by assessing coral recruitment rates and community composition.