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The immediate goal in the Reef Water Quality Protection Plan 2009 (Reef Plan) was:
“To halt and reverse the decline in water quality entering the reef by 2013.”

The long-term goal was:
“To ensure that by 2020 the quality of water entering the reef from adjacent catchments has no detrimental impact on the health and resilience of the Great Barrier Reef.”

Improvements in land management practices will take time to translate into improved marine condition as there are significant time lags between implementation and measurable outcomes in these natural systems. Inshore marine condition is also strongly influenced by episodic events such as tropical cyclones and floods which have impacted all regions in recent years.

It should be noted that the marine results focus mainly on the inshore area of the Great Barrier Reef. Water quality at mid and outer shelf sites is generally good to very good overall because it is less influenced by river discharges.


The Great Barrier Reef receives runoff from 35 major catchments which drain 424,000 square kilometres of coastal Queensland. The reef region is relatively sparsely populated; however, there have been extensive changes in land-use since European settlement in areas adjacent to the coast (Furnas, 2003; GBRMPA, 2012). Increasing pressure from human activities continues to have an adverse impact on the quality of water entering the reef lagoon, particularly during the wet season, even though some progress has been made in addressing this issue through Reef Plan. Flood waters deliver loads of nutrients and sediments to the reef that are well above natural levels and many times higher than in non-flood waters (Waters et al., 2014). Pesticides, which are manufactured chemicals with no natural level, are detected year-round in reef waters (Gallen et al., 2013). The main source of excess nutrients, fine sediments and pesticides from reef catchments is diffuse-source pollution from agriculture (The State of Queensland, 2013). Pollutant loads and the actions taken to reduce them are documented elsewhere in this report.

Disturbances affecting the Great Barrier Reef

The health and resilience of the reef is affected by a range of short-term acute and longer term chronic disturbances, including:

  • catchment runoff
  • floods
  • cyclones
  • crown-of-thorns starfish outbreaks
  • elevated sea surface temperatures.

A resilient coral community has high rates of recruitment and growth that compensate for losses resulting from the combination of acute disturbances (e.g. cyclones) and chronic environmental stressors (e.g. poor water quality). Over time, chronic stress may decrease the resilience of the reef ecosystem, by slowing or inhibiting recovery from acute disturbances. The impact of disturbances on the reef depends on their frequency, duration and severity, as well as the state of the ecosystem (Fabricius, 2005; Osborne et al., 2011). Multiple acute disturbances in close succession usually have a combined negative effect on reef resilience that is greater than the effect of each disturbance in isolation. Importantly, reducing one stress will often help the ecosystem recover from or resist the impact of other pressures. For example, improving water quality is expected to improve the resilience of corals to the effects of climate change.

Between 2006 and 2012, repeated disturbances had a considerable and widespread impact on the water quality and ecosystem status of the inshore area, as seen by the near loss of some seagrasses communities following the cyclones and floods in 2011. There are signs of recovery at some locations after a couple of years of less extreme weather events. However, marine ecosystem health remains vulnerable and it may take many years for complex communities to re-establish.

The Strategic Assessment Report (GBRMPA, 2013) and Outlook Report (GBRMPA, 2014 in press) concluded that the overall outlook for the reef is ‘poor’, and the health of the reef ecosystem is declining in inshore areas south of Cooktown. For example, coral cover on mid-shelf reefs along the developed coast of the central and southern Great Barrier Reef has declined to less than 50 per cent of what it was in 1985, while coral cover in the northern Great Barrier Reef has not shown the same consistent downward trend (De’ath et al., 2012). Outbreaks of the coral-eating crown-of-thorns starfish are one of the main causes of the decline in coral cover reef-wide, and the link between outbreaks and the level of nutrients in flood waters has been greatly strengthened (Fabricius et al., 2010; Furnas et al., 2013).

The area at highest risk from degraded water quality and its flow-on effects is the inshore region (Alvanez-Romero et al., 2013), which makes up approximately eight per cent of the Great Barrier Reef Marine Park. Inshore seagrass and coral reef ecosystems support significant ecological communities and the inshore region is the area most used by recreational visitors, commercial tourism operators and some commercial fisheries. Current management interventions are having a positive effect on water quality; however, it will take time and continued improvements in land management practices for the marine ecosystem to recover and return to good health.

Impacts of catchment runoff

Reef ecosystems and the catchments are part of a dynamic, interconnected system and the relationship between land use, water quality and ecosystem health indicators (e.g. coral cover and seagrass abundance) is relatively well understood. Nutrient enrichment, turbidity, sedimentation and pesticides all affect the resilience of the reef, degrading coral reefs and seagrass meadows at local and regional scales (reviewed in Brodie et al., 2012; The State of Queensland, 2013). Pollutants may also interact to have a combined negative effect on reef resilience that is greater than the effect of each pollutant in isolation. For example, the reduced light and excess nutrients found in turbid flood plumes combine to increase the level of stress on seagrasses (Collier et al., 2012; McKenzie et al., 2013) and differences in tolerance between species of coral to nutrient enrichment and sedimentation can lead to tissue death and changes in community composition (Fabricius, 2005; Fabricius, 2011; Weber et al., 2012). Since 2009, there has been a steady decline in key pollutant loads entering the reef lagoon. However, a sustained and greater effort will be needed to achieve the Reef Plan goal of no detrimental impact on the health and resilience of the reef.


In the summer of 2011-2012, discharge from many rivers in the central and southern areas of the reef was more than three times above the median discharge. The highest discharge was from the Burdekin and Fitzroy Rivers, and all rivers in the Mackay Whitsunday region (the Pioneer River had the highest proportional discharge at 3.8 times above the median). However, flows from all rivers were well below those in the 2010-2011 wet season, which was the second wettest since records began. River discharge was below the long-term median in the Cape York region and close to median levels in the Wet Tropics region.

Combined annual discharge from major rivers in each region, 2002–2013. Source: Data supplied by the Queensland Department of Natural Resources and Mines, compiled by the Australian Institute of Marine Science and McKenzie et al.

In the summer of 2012-2013, ex-Tropical Cyclone Oswald delivered above average rainfall to the entire reef catchment. This system tracked down the coast and flooded many rivers from Cairns to Bundaberg. All rivers from the Fitzroy in Rockhampton to around Maryborough suffered moderate to major flooding, and severe flooding occurred in the Burnett catchment. The Calliope, Boyne and Burnett Rivers also had above median discharge in 2012-2013.

In particular, the southern third of the Great Barrier Reef Marine Park (i.e. from the Whitsunday islands to Seventeen Seventy) was exposed to a large volume of low salinity flood waters, which is likely to have contributed to localised coral bleaching and mortality on shallow, inshore reefs in the area. In addition to large volumes of freshwater, wet season floods deliver the majority of nutrient, sediment and pesticide loads to the reef lagoon.


Three small (Category 1 or 2) cyclones traversed parts of the reef between 2011-2012 and 2012-2013. The most significant impacts were associated with the Category 1 Cyclone Oswald, largely after it was downgraded to a significant rain depression. The Great Barrier Reef Marine Park Authority’s Integrated Eye on the Reef monitoring network recorded some damage to reefs from Cairns to the Capricorn Bunker Group following ex-Tropical Cyclone Oswald, which traversed down the reef from north to south between 23 and 29 January 2013. The high winds and heavy rainfall associated with this event had the greatest effect on coral reefs and seagrass meadows in southern areas. These effects included physical damage from waves, as well as exposure to low salinity, high sediments and turbidity from the flood plumes.

Since 2005, many areas of the reef have been affected by cyclonic activity including very destructive category 4 or above cyclones. For example, about 13 per cent of the reef, representing a 300 kilometre stretch from Cairns to Townsville, was exposed to Tropical Cyclone Yasi's destructive or very destructive winds in February 2011.

Cyclones may cause extreme physical damage to reef structure and other benthic communities, such as seagrass meadows. The combined paths of all cyclones since 2005 have exposed 3889 reefs (80 per cent of the Great Barrier Reef Marine Park) to gale force winds or above. Most of the affected reefs were outside the inshore area, which is a relatively small proportion of the whole Great Barrier Reef Marine Park. Recent estimates attribute 48 per cent of total coral mortality recorded between 1985 and 2012 to cyclones and storms (De’ath et al., 2012).  There have been no large-scale assessments of the impacts on seagrass communities, but localised monitoring (PDF, 2.79 MB) after Cyclone Yasi suggests cyclones play a significant role in the redistribution of marine sediments by scouring the seafloor and removing benthic communities such as seagrass. The effect of multiple severe cyclones and floods on ecosystem health is still evident today (McKenzie et. al., 2013; Thompson et al., 2013). The extensive loss of seagrass across much of the southern part of the reef resulted in a large number of dugong and turtle deaths and the population of dugongs in the southern area of the reef is at a record low.

Extent of the Great Barrier Reef affected by Category 4 or 5 cyclones in the eight year period 2005-2013. Map: courtesy of the Spatial Data Centre, Great Barrier Reef Marine Park Authority.

Crown-of-thorns starfish

Crown-of-thorns starfish have had a major impact on the reef with an analysis of long-term monitoring data showing the starfish has been responsible for 42 per cent of coral cover loss since 1985 (De’ath et al. 2012).  Most outbreaks occur on mid-shelf reefs, beginning along the narrow northern shelf between Cairns and Lizard Island (the ‘initiation zone’) and then moving to southern reefs as larvae are transported by the East Australian Current. The Swains reefs in the Fitzroy region have had low-level chronic infestations throughout most of the past three decades, which is explained by the high density of coral and the regional oceanography.

In 2012-2013, crown-of-thorns starfish were recorded at outbreak densities on 30 per cent of reefs monitored by the Long Term (Reef) Monitoring Program.  Densities in the ‘initiation zone’ were at the highest levels since 1986 (Miller and Sweatman, 2013).

An active outbreak of crown-of-thorns starfish occurs when densities are such that the starfish consume coral tissue faster than the corals can grow. This is generally considered to be densities greater than about 15 starfish per hectare when coral cover is moderate to high (Moran and De’ath, 1992). However, many of the inshore and mid-shelf reefs that were affected by multiple severe weather events in recent years have lower coral cover and, therefore, reduced capacity to cope with these levels of starfish.

There are three previously documented outbreaks of crown-of-thorns starfish in the reef since the 1960s (1961-1968, 1978-1991 and 1993-2005), with the latest, ongoing outbreak commencing in 2011. The onset of the current outbreak is believed to be associated with the poor quality of water entering the reef following the floods and severe weather events in 2009 to 2011 (Brodie et al., 2005; Fabricius et al., 2010).

The Australian Government is committed to protecting coral cover at high value tourism sites from crown-of-thorns starfish through a diver injection control program. The control program has been underway since 2012 and is a collaborative effort involving the government, tourist operators including the Association of Marine Park Tourism Operators, researchers and volunteers. Monitoring will ascertain whether coral cover and diversity can be maintained at these sites.

Graph data (.csv, 1KB)

Elevated sea surface temperatures

Coral bleaching across the reef in 2011-2012 and 2012-2013 was generally low to moderate, though a single instance of a high level of impact was observed in the Mackay Whitsunday region in 2012-2013. Most of the bleached areas were in the Wet Tropics and the Mackay Whitsunday regions (GBRMPA, 2014). Over the summer, the accumulated heat stress was between 20 to 40 degree heating days on average. 

Coral bleaching commonly occurs when accumulated temperature stress, measured as degree heating days over the summer months, exceeds a threshold of about 60 to 100 degree heating days (Maynard, 2010). An increase in the long-term average temperature of reef waters is narrowing the gap between a regular summer and a coral bleaching season. For example, the frequency of mass bleaching events has increased over the last two decades, corresponding with higher seawater temperatures (Johnson and Marshall, 2007; Lough, 2007). Major coral bleaching events caused by unusually warm water temperatures had not been recorded in the Great Barrier Reef Marine Park before a major episode in 1998 that was part of a global event. Similar conditions returned in 2002 and to a lesser extent in 2006, and have caused substantial loss of coral cover (De’ath et. al., 2012). Prolonged exposure to elevated seawater temperatures may also increase the susceptibility of corals to disease (Bruno et. al., 2007).

Water temperature as degree heating days and areas where coral bleaching occurred.

Influence of climate change

The intensity of disturbances to the reef is set to increase under future climate change scenarios (Hoegh-Guldberg et al., 2007). The average annual seawater temperature on the reef is likely to rise by one to three degrees Celsius by 2100 (Intergovernmental Panel on Climate Change, 2007; Garnaut, 2008). It is also predicted that reef waters will become more acidic, sea levels will continue to rise, patterns of ocean circulation will change and weather events will become more extreme (Intergovernmental Panel on Climate Change, 2007). The extent and persistence of damage to the reef will largely depend on the rate and magnitude of change in the world’s climate and on the resilience of the reef ecosystem (GBRMPA, 2009). This has important implications for the future management of the Great Barrier Reef and run-off entering the reef lagoon. For example, modelling suggests that the upper thermal bleaching limit of corals is correlated with exposure to dissolved inorganic nitrogen and that reducing the output of dissolved inorganic nitrogen may enhance the resilience of inshore corals (Woodridge, 2009).

The future is not easily forecast, but there is strong evidence that halting and reversing the decline of water quality in the Great Barrier Reef lagoon will increase the natural resilience of reef ecosystems to these future challenges.

Regional results:


Álvarez-Romero, J.G., Devlin, M., Teixeira da Silva, E., Petus, C., Ban, N.C., Pressey, R.L., Kool, J., Roberts, J.J., Cerdeira-Estrada, S., Wenger, A.S., Brodie, J., 2013. A novel approach to model exposure of coastal-marine ecosystems to riverine flood plumes based on remote sensing techniques. Journal of Environmental Management 119, 194-207.

Brodie, J., Fabricius, K.E., De'ath, G., Okaji, K., 2005. Are increased nutrient inputs responsible for more outbreaks of crown-of-thorns starfish? An appraisal of the evidence. Mar. Pollut. Bull. 51, 266-278.

Brodie, J.E., Binney, J., Fabricius, K., Gordon, I., Hoegh-Guldberg, O., Hunter, H., O’Reagain, P., Pearson, R., Quirk, M., Thorburn, P., Waterhouse, J., Webster, I. and Wilkinson, S. 2008, Synthesis of evidence to support the Scientific Consensus Statement on water quality in the Great Barrier Reef, Reef Water Quality Protection Plan Secretariat, Brisbane.

Brodie, J.E., Kroon, F.J., Schaffelke, B., Wolanski, E.C., Lewis, S.E., Devlin, M.J., Bohnet, I.C., Bainbridge, Z.T., Waterhouse, J., Davis, A.M., 2012. Terrestrial pollutant runoff to the Great Barrier Reef: An update of issues, priorities and management responses. Marine Pollution Bulletin 65, 81-100.

Brodie, J., Waterhouse, J., Schaffelke, B., Kroon, F., Thorburn, P., Rolfe, J., Johnson, J., Fabricius, K., Lewis, S., Devlin, M., Warne, M. and McKenzie, L.J. 2013(a), 2013 Scientific Consensus Statement: Land use impacts on Great Barrier Reef Water Quality and Ecosystem Conditions, Reef Water Quality Protection Plan Secretariat, Brisbane.

Brodie, J., Waterhouse, J., Maynard, J., Randall, L., Zeh, D., Devlin, M., Lewis, S., Furnas, M., Schaffelke, B., Fabricius, K., Collier, C., Brando, V., McKensie, L., Warne, M.S.J., Smith, J., Negri, A., Henry, N., Petus, C., da Silva, E., Waters, D., Yorkston, H. and Tracey, D. , 2013(b), 'Reef Plan Scientific Consensus Statement - Assessment of the risk of pollutants to ecosystems of the GBR including differential risk between sediments, nutrients and pesticides and between land uses, industries and catchment, Environment and Heritage Protection, Brisbane

Bruno, J.F., Selig, E.R., Casey, K.S., Page, C.A., Willis, B., Harvell, C.D., Sweatman, H., Melendy, A.M., 2007. Thermal stress and coral cover as drivers of coral disease outbreaks. PLoS Biology 5, e124.
Bureau of Meteorology, 2010. Annual Climate Summary 2009.

Collier, C., Waycott, M., 2009. Drivers of change to seagrass distributions and communities on the Great Barrier Reef. Literature review and gaps analysis. Report to the Marine and Tropical Sciences Research Facility. 25, 55 p.

Collier, C.J., Waycott, M., Giraldo-Ospina, A., 2012. Responses of four Indo-West Pacific seagrass species to shading. Marine Pollution Bulletin 65, 342-354.

De’ath G, Fabricius KE, Sweatman H, Puotinen M (2012) The 27-year decline of coral cover on the Great Barrier Reef and its causes. Proceedings of the National Academy of Sciences 190(44):17995-17999

Fabricius, K.E., 2005. Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis. Mar. Pollut. Bull. 50, 125-146.

Fabricius, K.E., 2011. Factors determining the resilience of coral reefs to eutrophication: a review and conceptual model, in Dubinsky, Z., Stambler, N. (Eds.), Coral Reefs: An Ecosystem in Transition. Springer, Dordrecht, pp. 493-508.

Fabricius, K.E., Cséke, S., Humphrey, C., De’ath, G., 2013. Does Trophic Status Enhance or Reduce the Thermal Tolerance of Scleractinian Corals? A Review, Experiment and Conceptual Framework. PLoS ONE 8, e54399.

Fabricius, K.E., Okaji, K., De'ath, G., 2010. Three lines of evidence to link outbreaks of the crown-of-thorns seastar Acanthaster planci to the release of larval food limitation. Coral Reefs 29, 593-605.

Furnas, M., 2003. Catchments and Corals: Terrestrial Runoff to the Great Barrier Reef. Australian Institute of Marine Science, Townsville.

Furnas, M., Brinkman, R., Fabricius, K., Tonin, H., Schaffelke, B., 2013. Chapter 1: Linkages between river runoff, phytoplankton blooms and primary outbreaks of crown-of-thorns starfish in the Northern GBR. In: Assessment of the relative risk of water quality to ecosystems of the Great Barrier Reef: Supporting Studies. A report to the Department of the Environment and Heritage Protection, Queensland Government, Brisbane. TropWATER Report 13/30, Townsville, Australia.

Gallen, C., Devlin, M., Paxman, C., Banks, A., Mueller, J. (2013)  Pesticide monitoring in inshore waters of the Great Barrier Reef using both time-integrated and event monitoring techniques (2012 - 2013). The University of Queensland, The National Research Centre for Environmental Toxicology (Entox).

Garnaut, R., 2008. The Garnaut climate change review. , 634.

Great Barrier Reef Marine Park Authority, 2010. Water quality guidelines for the Great Barrier Reef Marine Park.

Great Barrier Reef Marine Park Authority, 2009. Great Barrier Reef Outlook Report 2009. , pp 192.

Great Barrier Reef Marine Park Authority, 2011. Extreme Weather and the Great Barrier Reef (PDF, 2 MB). GBRMPA, Townsville, Qld.

Great Barrier Reef Marine Park Authority 2012, Informing the outlook for Great Barrier Reef coastal ecosystems, GBRMPA, Townsville.

Great Barrier Reef Marine Park Authority, 2013. Great Barrier Reef Strategic Assessment Report, GBRMPA, Townsville, Qld.

Great Barrier Reef Marine Park Authority, 2014 (In Press) Great Barrier Reef outlook report 2009, GBRMPA, Townsville, Qld.

Hoegh-Guldberg, O., Mumby, P.J., Hooten, A.J., Steneck, R.S., Greenfield, P., Gomez, E., Harvell, C.D., Sale, P.F., Edwards, A.J., Caldeira, K., Knowlton, N., Eakin, C.M., Iglesias-Prieto, R., Muthiga, N., Bradbury, R.H., Dubi, A., Hatziolos, M.E., 2007. Coral reefs under rapid climate change and ocean acidification. Science (Wash.) 318, 1737-1742.

Hutchings, P., Haynes, D., 2005. Marine Pollution Bulletin Special Edition editorial. Mar. Pollut. Bull. 51, 1-2.

Intergovernmental Panel on Climate Change, 2007. Climate change 2007 synthesis report. Summary for policymakers. , 22p.

Johnson, J.E. and Marshall, P.A. (eds) 2007, Climate change and the Great Barrier Reef: a vulnerability assessment, Great Barrier Reef Marine Park Authority and Australian Greenhouse Office

Lough, J. 2007, Climate and climate change on the Great Barrier Reef, in Climate change and the Great Barrier Reef: A Vulnerability Assessment, eds J.E. Johnson and P.A. Marshall, Great Barrier Reef Marine Park Authority and Australian Greenhouse Office, Townsville, pp. 15-50

Magnusson, M., Heimann, K., Quayle, P., Negri, A.P., 2010. Additive toxicity of herbicide mixtures and comparative sensitivity of tropical benthic microalgae. Mar. Pollut. Bull. 60, 1978-1987.

Maynard, J.A. 2010, Evaluation of thermal stress thresholds at the Australian Institute of Marine Science (AIMS) Long-Term Monitoring Program (LTMP) sites and Eye on the Reef tourism sites. Maynard Marine Consulting, Inc., Australia.

McCulloch, M., Fallon, S., Wyndham, T., Hendy, E., Lough, J.M., Barnes, D., 2003. Do sediments sully the reef? Ecos 115, 37-41.

McKenzie, L.J., Collier, C. and Waycott, M. 2012, Reef Rescue Marine Monitoring Program: Inshore seagrass, annual report for the sampling period 1st July 2010 – 31st May 2011, Fisheries Queensland, Cairns

Miller, I.R. and Sweatman, H. 2013. The status of crown-of-thorns starfish populations on the Great Barrier Reef from AIMS surveys. Report to the National Environmental Research Program. Reef and Rainforest Research Centre Limited, Cairns.

Moran,P.J.; and De'ath,G, 1992, Estimates of the abundance of the crown-of-thorns starfish Acanthaster planci in outbreaking and non-outbreaking populations on reefs within the Great Barrier Reef, Marine Biology 113, pp 509-515.

Moss, A.J., Rayment, G.E., Reilly, N., Best, E.K., 1992. Sediment and Nutrient Exports from Queensland Coastal Catchments, A Desk Study.

Neil, D.T., Orpin, A.R., Ridd, P.V., Yu, B., 2002. Sediment Yield and impacts from river catchments to the Great Barrier Reef Lagoon. Marine and Freshwater Research 53, 000-000.

Osborne, K., Dolman, A.M., Burgess, S.C., Johns, K.A., 2011. Disturbance and the dynamics of coral cover on the Great Barrier Reef (1995–2009). PLoS ONE 6, e17516.

Rohde, K., Masters, B., Fries, N., Noble, R. and Carroll, C. 2008. Fresh and marine water quality in the Mackay Whitsunday region; 2004/05 to 2006/07. Queensland Department of Natural Resources and Water for the Mackay Whitsunday Natural Resource Management Group, Australia.

Sweatman, H., Cheal, A.J., Coleman, G.J., Emslie, M.J., Johns, K., Jonker, M., Miller, I.R., Osborne, K., 2008. Long-term monitoring of the Great Barrier Reef: status report 8.

The State of Queensland 2013, Scientific Consensus Statement 2013. Chapter 1 Marine and coastal ecosystem impacts.

van Dam, J.W., Negri, A.P., Mueller, J.F., Uthicke, S., 2012. Symbiont-specific responses in foraminifera to the herbicide diuron. Mar. Pollut. Bull. in press.

Waters, D.K., Carroll C., Ellis, R., Hateley L., McCloskey J., Packett R., Dougall C., Fentie B.(2014). Modelling reductions of pollutant loads due to improved management practices in the Great Barrier Reef Catchments – Whole of GBR, Volume 1. Department of Natural Resources and Mines. Technical Report (ISBN: 978-1-7423-0999)

Waycott, M., McKenzie, L.J., 2010.  Final report project 1.1.3 to the Marine and Tropical Sciences Research Facility: Condition, trend and risk in coastal habitats: Seagrass indicators, distribution and thresholds of potential concern.

Weber, M., de Beer, D., Lott, C., Polerecky, L., Kohls, K., Abed, R., Ferdelman, T., Fabricius, K., 2012. A series of microbial processes kills corals exposed to organic-rich sediments. Proceedings of the National Academy of Sciences of the United States of America 109, E1558-E1567.

Last updated:
1 September, 2015

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