The AIMS Long Term Monitoring Program (LTMP) has been surveying the health of 47 reefs in the Great Barrier Reef annually since 1993. This represents the longest continuous temporal record of change in reef communities over such a large scale.

A team of trained divers surveys fishes by underwater visual census and records corals and other benthic organisms along the same sections of reef at each visit. The data captures the natural variability of coral and fish populations and documents the effects of disturbances like crown-of-thorns starfish (COTS), cyclones and bleaching events .

The team also provides situational awareness on threats to the reef, such as outbreaks of COTS and coral disease , monitors the effects of the 2004 zoning plan and gathers information on other issues of concern to reef managers.

The LTMP publishes regional reports after each survey trip. Information on each survey reef is available on the internet and is updated after each visit. GBR status reports are produced every two years.

In Western Australia, AIMS has been monitoring fish and coral communities on Scott Reef in the north-west since 1994 to understand natural variability, and how its isolation from other reefs in the Indian Ocean and dependence upon self-recruitment affects the dynamics of local populations and resilience of communities to disturbances like cyclones.