Coral reefs around the world and the populations who directly and indirectly depend on them are facing a multitude of global, regional, and local threats. In face of these unprecedented global changes, it is critical to understand how coral reef ecosystems and the goods and services they provide will evolve. The problem is complex and its solution is difficult because of the nature of biophysical connectivity of coral reef systems, and their connection with human social and economic systems. In order to increase our knowledge and the predictive capacities necessary to determine how coral reef ecosystems will respond to global change, it is necessary to employ a combination of data synthesis and numerical simulation. The increase in the knowledge base and predictive capacities regarding the influence of the drivers: ocean circulation, climate, ocean-acidification, terrestrial run-offs driven by enhanced human activities such as the clearing of native vegetation and its replacement with intensive agriculture and coastal development, pollution, overfishing, and invasive species on marine coral reef ecosystems is central for the effective management and conservation of coral reef ecosystem services. Modeling at multiple scales has revealed to be a vital tool in meeting this challenge by providing important technology that allows managers, other decision makers, and users to see the dynamics of the whole system – including ecological, biophysical, socioeconomic, and restoration aspects. The aim of this review is to provide information concerning the studies of local and regional coral reef ecosystem models, the coupling of ecological and social system models and models based on ecosystems as well as to provide suggestions for future development and use of models for science-based management of global change.