A five-year period (2002–2006) of below-median rainfall followed by a six-year period (2007–2012) of above-median rainfall and seasonal flooding allowed a natural experiment into the effects of runoff on the water quality and subsequent coral community responses in the Whitsunday Islands, Great Barrier Reef (Australia). Satellite-derived water quality estimates of total suspended solids (TSS) and chlorophyll-a (Chl) concentration showed marked seasonal variability that was exaggerated during years with high river discharge. During above-median rainfall years, Chl was aseasonally high for a period of 3 months during the wet season (February–April), while TSS was elevated for four months, extending into the dry season (March–June). Coinciding with these extremes in water quality was a reduction in the abundance and shift in the community composition, of juvenile corals. The incidence of coral disease was at a maximum during the transition from years of below-median to years of above-median river discharge. In contrast to juvenile corals, the cover of larger corals remained stable, although the composition of communities varied along environmental gradients. In combination, these results suggest opportunistic recruitment of corals during periods of relatively low environmental stress with selection for more tolerant species occurring during periods of environmental extremes.

River runoff and associated flood plumes (hereafter river plumes) are a major source of land-sourced contaminants to the marine environment, and are a significant threat to coastal and marine ecosystems worldwide. Remote sensing monitoring products have been developed to map the spatial extent, composition and frequency of occurrence of river plumes in the Great Barrier Reef (GBR), Australia. There is, however, a need to incorporate these monitoring products into Risk Assessment Frameworks as management decision tools. A simple Satellite Risk Framework has been recently proposed to generate maps of potential risk to seagrass and coral reef ecosystems in the GBR focusing on the Austral tropical wet season. This framework was based on a “magnitude × likelihood” risk management approach and GBR plume water types mapped from satellite imagery. The GBR plume water types (so called “Primary” for the inshore plume waters, “Secondary” for the midshelf-plume waters and “Tertiary” for the offshore plume waters) represent distinct concentrations and combinations of land-sourced and marine contaminants. The current study aimed to test and refine the methods of the Satellite Risk Framework. It compared predicted pollutant concentrations in plume water types (multi-annual average from 2005–2014) to published ecological thresholds, and combined this information with similarly long-term measures of seagrass and coral ecosystem health. The Satellite Risk Framework and newly-introduced multi-annual risk scores were successful in demonstrating where water conditions were, on average, correlated to adverse biological responses. Seagrass meadow abundance (multi-annual change in % cover) was negatively correlated to the multi-annual risk score at the site level (R² = 0.47, p < 0.05). Relationships between multi-annual risk scores and multi-annual changes in proportional macroalgae cover (as an index for coral reef health) were more complex (R² = 0.04, p > 0.05), though reefs incurring higher risk scores showed relatively higher proportional macroalgae cover. Multi-annual risk score thresholds associated with loss of seagrass cover were defined, with lower risk scores (≤0.2) associated with a gain or little loss in seagrass cover (gain/−12%), medium risk scores (0.2–0.4) associated with moderate loss (−12/−30%) and higher risk scores (>0.4) with the greatest loss in cover (>−30%). These thresholds were used to generate an intermediate river plume risk map specifically for seagrass meadows of the GBR. An intermediate river plume risk map for coral reefs was also developed by considering a multi-annual risk score threshold of 0.2—above which a higher proportion of macroalgae within the algal communities can be expected. These findings contribute to a long-term and adaptive approach to set relevant risk framework and thresholds for adverse biological responses in the GBR. The ecological thresholds and risk scores used in this study will be refined and validated through ongoing monitoring and assessment. As uncertainties are reduced, these risk metrics will provide important information for the development of strategies to manage water quality and ecosystem health.

Coral reef management is increasingly focused on supporting the resilience of coral communities to increasing and cumulative pressures. The coral index provides a concise summary of coral community resilience that can be efficiently communicated to a range of management and policy stakeholders. We detail the development of the index both as a technical reference for users but also as an example of an approach that could be more generally applied to the reporting of ecosystem resilience. The index is sensitive to acute impacts that are expected when coral communities are exposed to disturbances such as cyclones, bleaching events or crown-of-thorns outbreaks. Importantly, spatial and temporal trends in the index enable the identification of areas and periods of reduced resilience that suggest chronic environmental pressure imposed by runoff. The ability to summarise complex ecological processes into a single index provides an efficient and intuitive tool for the communication of where, when and which pressures are impacting ecosystem resilience.

Changes in coral reef health and status are commonly reported using hard coral cover, however such changes may also lead to substantial shifts in coral community composition. Here we assess the extent to which coral communities departed from their pre-disturbance composition following disturbance (disassembly), and reassembled during recovery (reassembly) along an environmental gradient across the continental shelf on Australia’s Great Barrier Reef. We show that for similar differences in coral cover, both disassembly and reassembly were greater on inshore reefs than mid- or outer-shelf reefs. This pattern was mostly explained by spatial variation in the pre-disturbance community composition, of which 28% was associated with chronic stressors related to water quality (e.g., light attenuation, concentrations of suspended sediments and chlorophyll). Tropical cyclones exacerbated the magnitude of community disassembly, but did not vary significantly among shelf positions. On the outer shelf, the main indicator taxa (tabulate Acropora) were mostly responsible for community dissimilarity, whereas contribution to dissimilarity was distributed across many taxa on the inner shelf. Our results highlight that community dynamics are not well captured by aggregated indices such as coral cover alone, and that the response of ecological communities to disturbance depends on their composition and exposure to chronic stressors.

Coral reefs are under increasing pressure from a variety of stressors, highlighting the need for information about the status of coral reef communities including the distribution, abundance and composition of juvenile and adult coral assemblages. This information is currently limited for the Great Barrier Reef (GBR) and is necessary for understanding the impacts of disturbances and the system’s potential for recovery. This study reports juvenile and adult hard coral abundance and composition from 122 reefs on the GBR during a period of limited acute disturbance. The data represent baseline observations for juvenile hard coral assemblages spanning the longitudinal cross-shelf gradient of the GBR and 12 degrees of latitude and augment reported distribution of adult coral assemblages over the same scale with inclusion of additional reefs. Juvenile and adult coral assemblages reflected broad differences imposed by the gradient of environmental conditions across the GBR. The mean density of juvenile hard corals was lower in the inshore reefs (5.51 m²) than at either the mid-shelf (11.8 m²) or outer shelf reefs (11.2 m²). The composition of juvenile and adult coral assemblages covaried overall, although there were different relationships between these two life stages across the continental shelf and among community types. Dissimilarity between juvenile and adult coral assemblages was greater on inshore and outer shelf reefs than on reefs in the mid-shelf, although, there were differences in community types both within these shelf positions and those that spanned mid- and outer shelf reefs. Dissimilarity was greatest for Inshore branching Acropora and high for Southern Acropora communities, although very high coral cover and very low juvenile densities at these reefs precluded interpretation beyond the clear competitive dominance of Acropora on those reefs. Dissimilarity was also high between juvenile and adult coral assemblages of Turbid inshore communities suggesting water quality pressures, along with synergistic effects of other stressors, pose ongoing selective pressures beyond the juvenile stage. Conversely, relatively low dissimilarity between juvenile and adult coral assemblages on mid-shelf and lower latitude outer shelf reefs suggests pressures beyond those influencing settlement and early post-settlement survival were having less influence on the composition of adult coral assemblages.