Coral reefs have enormous ecological, economic and cultural value, but are threatened by natural disturbances and human activities including those causing global-scale changes. Worldwide, corals increasingly are being replaced by macroalgae or non-coral invertebrates. The reefs of Moorea, French Polynesia, provide an ideal model system to understand factors that mediate ecological resilience and to develop the capacity to forecast the composition and function of reefs in a future ocean of warmer water and a lower pH. The overarching goal of the Moorea Coral Reef (MCR) LTER, established in 2004, is to gain a predictive understanding of the dynamics and functionality of oceanic coral reef ecosystems. MCR science achieves this goal through long-term observations, experiments and modeling. Changes in community structure revealed by the time series are used to generate hypotheses, which are tested using process-oriented studies including long term experiments. Empirical studies are synthesized and modeled to gain novel insight into the responses of coral reefs of Moorea to changing environmental conditions, to search for ecological generality, and to advance ecological theory.