This page has been archived and kept as a reference. Content on this page may be out of date.

It is not possible to test and monitor water quality at all places at all times, but there are ways to indirectly infer water quality using "bioindicators". These are organisms, chemical markers or biological processes whose change points to altered environmental conditions. While direct sampling provides information about the conditions at the time of sampling only, bioindicators provide a time-integrated estimate of past environmental conditions.

Time scales can depend on the actual indicator chosen. They therefore serve to detect changes in water quality even when water quality measurements are not available or are too variable.

For example, a reduced abundance of large foraminifera (marine micro-organisms) or the darkening of coral pigmentation may indicate that a reef has been exposed to poor water quality for several weeks or months.

Bioindicators can also provide information on the harmful effects of contaminants at biochemical, molecular and cellular levels and can act as an early warning system for larger-scale effects. For example, reduced photosynthesis in a plant or a coral may indicate stress from exposure to herbicides. Researchers at AIMS have investigated stress from exposure to contaminants in corals, fish, foraminifera, biofilms and microalgae.

Barramundi and mud skippers appear also to be sensitive bioindicator species. Monitoring of biochemical, cellular or genetic changes in fish tissue using sensitive new techniques can help identify if changes are due to natural variation or human-induced effects.

Public debate on water quality in the Great Barrier Reef World Heritage Area has prompted AIMS to investigate the effects of water quality on many aspects of coral reef communities. The research indicates that coral reef communities in waters with high nutrients and turbidity, as often found near catchments with significant agricultural development, have a lower coral diversity and more macroalgae compared with those in remote areas.

While many of the AIMS studies are carried out in the field, validation experiments and methods development are undertaken in flow-through seawater facilities in the AIMS laboratories, where water quality, temperature and light can be carefully controlled.


Fabricius KE, Uthicke S, Cooper TF, Humphrey CA, De'ath AG and Mellors J (2007) Candidate bioindicator measures to monitor exposure to changing water quality on the Great Barrier Reef. Interim Report.. Catchment to Reef Research Program - CRC Reef and Rainforest CRC and Australian Institute of Marine Science. 225 p.

To download go to:

Gilmour JP, Cooper TF, Fabricius KE and Smith LD (2006) Early warning indicators of change in corals and coral communities responding to anthropogenic stressors in the Pilbara, Western Australia. Environmental Protection Authority, Western Australia. 100 p. To download, go to: