Coral reefs are in crisis. Globally, our reefs are degrading at an accelerating rate and present methodologies for coral-reef 'health' assessment, although providing important information in describing these global declines, have been unable to halt these declines. These assessments are usually employed with no clear purpose and using uncorrelated methods resulting in a failure to prevent or mitigate coral reef deterioration. If we are to ever successfully intervene, we must move beyond the current paradigm, where assessments and intervention decisions are based primarily on descriptive science and embrace a paradigm that promotes both descriptive and mechanistic science to recognize a problem, and recognize it before it becomes a crisis. The primary methodology in this alternative paradigm is analogous to the clinical and diagnostic methodologies of evidence-based medicine. Adopting this new paradigm can provide the evidence to target management actions on those stressors currently impacting reef ecosystems as well as providing a means for proactive management actions to avert irreversible habitat decline.