Increasing human pressures on marine ecosystems raise the need to monitor the response of marine organisms over broad spatial and temporal scales in order to evaluate regional changes in habitat condition and population trends. This report presents findings about the status and trends of coral and rocky reef biodiversity around Australia, inferred from the integration of three long-term monitoring programs that repeatedly surveyed benthic, fish and invertebrate communities at a total of >3000 sites distributed around the continent. Based on these integrated long-term surveys, we modelled trends in individual reef species, as well as those in biodiversity indicators that can be linked to pressures such as exploitation or global warming.