AIMS research into the “Effects of water quality on coral reefs” under the CRC Reef research banner concluded in 2006–2007 after a sustained effort over six years. Between 2003 and 2006 it was enhanced by supplementary funding from partnership with the joint Rainforest CRC and CRC Reef “Catchment to Reef” programme. The research programme resulted in significant advances in understanding of the relationships between water quality and the condition of inshore coral reefs and also developed a suite of bio-indicators for changes in water quality, ranging from molecular stress markers to indicators of general ecosystem health. Outputs included training 14 postgraduate students and 34 published works covering macroalgae, coralline algae, coral reproduction, soft and hard coral biodiversity patterns, biofilms, marine snow, sediment resuspension, a review of the effects of terrestrial runoff, and a new method to assess causality in ecological studies.

Collectively the research contributed substantially, over a relatively short period of time, to a shift in the public discourse about water quality on the Great Barrier Reef from strongly polarised positions (“no hope” versus “no problem”) to a more informed one about the subtle effects of variable water quality on the condition and ecological functions of inshore reef ecosystems. This impact was achieved through sustained scientific publication, conference presentations, and public education through presentations and discussions at public meetings, and print, film and electronic media. The results were presented extensively to GBRMPA, and  featured in the Productivity Commission Report and the Baker Report on the issue of land run-off. This high level of public awareness has led to the response by State and Commonwealth Governments in such initiatives as the GBR Water Quality Protection Plan (Reef Plan), which seeks to halt or reverse declining water quality in inshore sections of the Great Barrier Reef Marine Park.

Research into water quality and ecosystem health continues to be a core activity of AIMS. Research includes delving deeper into the ecological processes causing the observed responses to water quality, further refinement of bioindicators for water quality with a focus on dose-response relationships, exploring the interaction of water quality with other stressors such as climate change, the wider effects of water quality on the biodiversity of coral reefs and broad-scale monitoring of water quality and ecosystem health as part of the Great Barrier Reef Water Quality Protection Plan (see AIMS research plan).

Divers deploying a sediment trap on a near-shore reef.