Principal water quality influences on Great Barrier Reef ecosystems

Corals and other reef organisms are influenced by a range of water quality variables. In general, they are adapted to tolerate variations in water quality, however when critical thresholds are exceeded they may be adversely impacted. Major water quality variables affecting coral reef health include water temperature, salinity, nutrient and suspended sediment concentrations, as well as toxicants including pesticides.


River discharges are the single biggest source of nutrients to the inshore areas of the Great Barrier Reef World Heritage Area. Most of the nutrients are discharged to the Great Barrier Reef World Heritage Area during tropical monsoon flood flows. Elevated nutrient concentrations result in a range of impacts on coral communities, and under extreme situations can result in coral reef community collapse. Elevated nutrient concentrations affect corals by promoting phytoplankton growth, which in turn supports increased numbers of filter feeding organisms such as tubeworms, sponges and bivalves that compete with coral for space. Macroalgal blooms can also result under enhanced nutrient regimes and macroalgae may overgrow coral structures, out-competing coral for space and shading coral colonies to critical levels.

Excessive phosphorus concentrations result in coral colonies with less dense, and hence weakened skeletons, which make colonies more susceptible to damage from storm action. Additionally, neither macroalgae nor most filter feeders add to reef consolidation through calcification. Elevated nutrients can inhibit fertilisation rates and embryo formation of corals, as well as causing direct coral mortality.

Sediments and Turbidity

Offshore coral reef environments are generally regarded as being adapted to low turbidity and low-nutrient conditions. In contrast, nearshore and coastal reef systems have evolved in relatively turbid environments where suspended sediment and turbidity are primarily influenced by local wind and wave regimes rather than by sediment supply. However, excessive inputs of sediment from the land to coral reefs can lead to reef destruction through burial, disruption of recruitment success or deleterious community shifts. Sediment affects coral by: smothering when particles settle out (sedimentation), reducing light availability (turbidity) and potentially reducing coral photosynthesis and growth. Elevated sediment and nutrient concentrations can also be deleterious to seagrass beds as they can cause a dramatic reduction of water column light penetration, which limits the seagrasses ability to manufacture food.



Impacted inshore reefs in the Wet Tropics region

(photos: K.Fabricius, Reef CRC/AIMS)


Reef corals exist in seawater salinities ranging from 25 to 42‰. At the lower end of the salinity tolerance range, following storm and flood events, corals can be killed by “freshwaters”. Symptoms of coral stress caused by lowered salinities include excessive mucous release and loss of zooxanthellae (bleaching). Salinity impacts to corals are increased by other flood related stresses such as sedimentation, turbidity and increased ultraviolet radiation exposure. For example, shallow reefs in the Great Barrier Reef Marine Park Keppel Island region suffered almost complete mortality due to prolonged salinity stress following the 1991 Fitzroy River floods, and 50% of the fringing reefs around Great Barrier Reef Snapper Island were killed by freshwater flood run-off in 1998.

Other Pollutants

Agriculture, urban settlement and industrial activities around the world have contributed to the widespread contamination of global marine ecosystems with pesticide residues, organochlorine compounds and heavy metals. These types of pollutants are persistent, highly toxic and many are essentially permanent additions to the environment.

Organochlorine Pesticides

Organochlorines are carbon-based chemicals that contain bound chlorine. These compounds are mostly artificial and enter the environment mainly through human activities. Chlorinated organic compounds have had a wide range of industrial and agricultural applications, although many of them are now banned from use. They include pesticides such as DDT (dichloro-diphenyl-trichloroethane) and lindane (g-HCH or gamma-hexachlorocyclohexane), and polychlorinated biphenyls (PCBs), which are also used in a range of industrial applications including dielectrics in electrical transformers. Pesticides and PCBs have been implicated in reproductive and immunological abnormalities observed in terrestrial bird populations and in marine mammal populations. While the impact of organochlorines are still unclear for lower invertebrates such as corals, there potential toxicity to immune systems and reproductive processes is of concern.

A number of new generation insecticides and herbicides are now used by the Queensland agricultural industry. Insecticides in use include chlorpyrifos and herbicides in use include atrazine, diuron, 2,4-D, glyphosate and paraquat. Chronic herbicide exposure from agricultural run-off has the potential to harm seagrasses and other photo-autotrophic reef organisms, including corals.

Heavy Metals

Heavy metals are natural constituents of rocks and soils and enter the environment as a consequence of weathering and erosion. Many metals are biologically essential, but all have the potential to be toxic to biota above certain threshold concentrations. Following industrialisation, unnatural quantities of metals have been released, and continue to be released into the aquatic environment through agricultural, urban stormwater and wastewater discharges. Zinc and copper are used in small amounts as fertilisers in some soils deficient in these elements, and arsenic, cadmium and mercury are constituents of some fungicides. Copper is also used as an algaecide and cadmium and zinc occur as contaminants of phosphatic fertilisers. Organism growth, reproduction and behaviour are affected by elevated metal concentrations.

Global Atmospheric Changes

Naturally occurring gases in Earth’s atmosphere act as a blanket around the earth, and help maintain its temperature. This is known as the greenhouse effect. Since the Industrial Revolution, large quantities of these ‘greenhouse gases’ such as carbon dioxide, methane, and nitrous oxide have been added to Earth’s atmosphere as a consequence of human activity. This has led to an increase in the amount of heat from solar radiation trapped by Earth’s atmosphere, leading to warmer global temperatures. Atmospheric carbon dioxide levels are expected to reach double pre-industrial levels by the year 2065. It is predicted that Earth’s temperature will continue to rise by approximately 0.3 º C per decade as a consequence of increased atmospheric concentrations of greenhouse gases, and this is estimated to result in an increase in sea temperature of 1-2º C by 2100. Altered global atmospheric changes have a range of potential impacts on tropical seas including:

Elevated concentrations of carbon dioxide in the atmosphere and dissolved in seawater.

Increased carbon dioxide concentrations in seawater enhance the dissolution of calcium carbonate, which makes up the coral skeleton. This may reduce calcification rates in coral, resulting in weakened skeletons and susceptibility to erosion of coral communities. This may lead to changes in coral community structure, reproduction and overall functioning in coral reef environments.

Elevated seawater temperatures.

Elevated water temperatures cause corals to be physiologically stressed, which upset the critical balance that maintains their symbiotic relationship with the algae (zooxanthellae) that inhabit the coral. When this occurs, the corals lose their colour, becoming bleached. The recognised biological effects of bleaching are reduced coral growth and calcification, reduced reproductive output and increased mortality. Corals will die if the stress is prolonged. The ecological consequences of bleaching include shifts in community structure and decreases in both species and habitat diversity.

Coral Bleaching at Magnetic Island – February 1998

Sea level rise due to melting polar ice.

Rising sea levels will have serious impacts on sand cays and coral reef islands, as rising sea water levels will contaminate freshwater lenses which support terrestrial vegetation in these environments.

Another predicted atmospheric change is the continuing loss of Earth’s ozone layer. The ozone layer absorbs a majority of the ultraviolet light entering Earth’s atmosphere. Ozone is destroyed naturally, but the rate of destruction is being accelerated by the release of chemicals such as chlorofluorocarbons (CFCs). It is predicted that this would increase the amount of ultraviolet light reaching earth. Ultraviolet light has a variety of destructive effects on marine life, and increased ultraviolet light will increase the severity of a coral bleaching event in the presence of high water temperatures.


Shipping is the major means of transporting cargo to and from Australia. Accidents resulting from groundings, vessels sinking, illegal and accidental oil and diesel spills, and loss of litter overboard can pollute the Great Barrier Reef World Heritage Area.  The threat is largely a function of environmental and socio economic vulnerability, vessel quality, types of oils and cargo carried, navigational hazards, weather, shipping density and standards of crewing.                            

Since 1987 over 600 shipping and boating incidents have been reported, including ship groundings, collisions, sinking’s and minor oil spill pollution events.  During this time period only 33 reported incidents were considered major and these included 11 collisions and 22 groundings.  Fortunately none of these incident resulted in a major oil spill pollution event.

Great Barrier Reef World Heritage Area shipping transit routes (Click to see larger view)


When a ship runs aground it has the potential to release large, concentrated quantities of antifoulant chemicals. Antifoulants are used on ships to control marine fouling (the growth of marine life on the hull of a ship). The antifoulants used on ships are predominately a combination of copper and tributyltin (TBT). Antifoulants are highly toxic, and the release of antifoulants represents a significant risk to marine life. Elevated levels of both copper and TBT have been detected in several commercial harbours and marinas in the central and northern Great Barrier Reef World Heritage Area. Sites away from the mainland are usually uncontaminated with either of these compounds.

Ballast Water and Ship Fouling

Ballast water is used to alter the draft, trim and stability of a ship when steaming and during cargo loading and unloading operations at port and at sea. Introduction of exotic marine species via ships’ ballast water has become a major environmental concern as it poses threats to local biodiversity, fisheries and aquaculture. The number of exotic marine “pests” introduced to Australian waters via ballast water discharges and ship hull fouling is reported to be more than 250 different species. Fifteen introduced species have been recorded for Queensland Ports. The majority of overseas bulk carriers that arrive in Queensland ports are from Korea and Japan. These bulk carriers pose a relatively low risk of introducing a pest species as they originate from ports that contain relatively cool waters, and the pest species would not be expected to survive in Queensland tropical waters (Hilliard and Raaymakers 1997). The exceptions are shipping arriving from the Southern Japanese ports, and ports in Singapore and Taiwan. These ports are all located in warmer waters and present a greater risk to sourcing species with the ability to survive in warmer tropical waters and become a local pest.

Table 2: Estimates of ballast water discharged to major ports (Hilliard and Raaymakers 1997)

Port Number of ships Ballast water discharged (Tonnes)
Hay Point 439 14,000,000
Gladstone 267 4,300,000
Abbot Point 67 2,000,000
Townsville 64 650,000
Mackay 34 280,000
Cape Flattery 27 430,000
Cairns 27 225,000
Mourilyan 25 194,000
Lucinda 17 168,000
Bundaberg 8 65,000
Port Alma 6 17,000

To address the ecological problems caused by marine pests, the National Introduced Marine Pests Co-ordination Group (NIMPCG) has developed a strategic plan aimed at developing a single management regime for the prevention and management of marine pest incursions. Key aspects of the plan include: prevention; emergency response; management of established introduced pests and governance.

Oil spills

Oil spills resulting from deliberate or accidental release of oils from ships or following a collision or grounding is one of the biggest threats to the Reef. During an oil spill a mixed petroleum product is released into the marine environment. The oil may eventually settle out of the water column onto the sediment or could be washed up onto beaches, reefs, mangroves and seagrass beds. A large range of vessels use the Great Barrier Reef Marine Park in the course of their daily activities from commercial fisheries, tourism vessels to large ocean going trading vessels. These vessels handle a range of fuels and generate a number of waste materials. Two hundred and eighty two confirmed vessel spills were recorded in the Great Barrier Reef World Heritage Area between 1987 and 2002.


Dumping of rubbish and other debris from ships into the marine environment has become an increasingly serious problem. Discarded debris can have a range of environmental consequences. It can entangle wildlife, causing death, limb amputation, drowning or strangulation in larger marine animals. Debris can also be ingested and cause internal blockages (especially in turtles) resulting in starvation and other complications. There is also an economic impact of debris and rubbish accumulation on beaches, predominantly the cost of removal and the loss of aesthetic values in recreational areas that are reliant on tourism-generated income.

Vessel Sewage

Marine Sewage contains pathogens that can affect human health by spreading hepatitis, gastrointestinal disease, causing skin infections and contributing to respiratory problems. The high concentration of nutrients in sewage can also effect coral reef and near shore environments by contributing to algal blooms, algal overgrowth and weakening of the coral skeleton.

The amount of sewage discharged from vessels within the Great Barrier Reef World Heritage Area is increasing. Currently, approximately 80,000 registered recreational vessels and roughly 3000 registered commercial vessels have access to the Great Barrier Reef World Heritage Area. The number of recreational vessels that can access the Great Barrier Reef World Heritage Area has grown at a rate of 4% to 7% per annum in recent years. This could lead to an increase in nutrient and coliform load on the Great Barrier Reef World Heritage Area ecosystem, particularly in frequently visited areas.

New vessel sewage regulations for the Great Barrier Reef Marine Park were introduced on 1 January 2005.

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