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The impact of physico-chemical factors on percent coral cover and coral health was examined on a spatial basis for two dominant  Acropora  species,  A. digitifera  and  A. spicifera,  at Ningaloo Reef (north-western Australia) in the southeast Indian Ocean. Coral health was investigated by measuring metabolic indices (RNA/DNA ratio and protein concentration), energy levels (lipid ratio) and autotrophic indices (chlorophyll  a  (chl  a ) and zooxanthellae density) at six stations during typical seasons (austral autumn 2010 (March and April), austral winter 2010 (August)) and during an extreme La Niña event in summer 2011 (February). These indices were correlated with 15 physico-chemical factors (measured immediately following coral sampling) to identify predictors for health indices. Variations in metabolic indices (protein concentration and RNA/DNA ratio) for  A. spicifera  were mainly explained by nitrogen, temperature and zooplankton concentrations under typical conditions, while for  A. digitifera , light as well as phytoplankton, in particular picoeukaryotes, were important, possibly due to higher energy requirement for lipid synthesis and storage in  A. digitifera . Optimum metabolic values occurred for both  Acropora  species at 26–28°C when autotrophic indices (chl  a  and zooxanthellae density) were lowest. The extreme temperature during the La Niña event resulted in a shift of feeding modes, with an increased importance of water column plankton concentrations for metabolic rates of  A. digitifera  and light and plankton for  A. spicifera . Our results suggest that impacts of high sea surface temperatures during extreme events such as La Niña may be mitigated via reduction on metabolic rates in coral host. The high water column plankton concentrations and associated low light levels resulted in a shift towards high symbiont densities, with lower metabolic rates and energy levels than the seasonal norm for the coral host.

Which Environmental Factors Predict Seasonal Variation in the Coral Health of Acropora digitifera and Acropora spicifera at Ningaloo Reef?