Coral reefs worldwide are being degraded by human-induced disturbances, resulting in ecological, economic, and cultural losses. Runoff and sedimentation are among the greatest threats to the coastal reefs surrounding high islands and adjacent to continental landmasses. Existing scientific data identify the key stressors, synergisms, and outcomes at the coral reef ecosystem, community, and population levels. These data demonstrate that marine protected areas alone may be insufficient for coral reef protection; integrated watershed management practices are also needed. Gaps in the effectiveness of environmental policy, legislation, and regulatory enforcement have resulted in the continued degradation of US and Australian reefs. Several Pacific islands, with intact resource stewardship and traditional leadership systems, have been able to apply research findings to coral reef management policies relatively quickly. Three case histories in Micronesia provide insight into how social sciences and biophysical data can be combined to manage human behaviors responsible for coral reef destruction.