The Reefs at Risk analysis produced a map-based indicator of potential threats to coral reefs. In order to capture the potential threats to coral reefs from coastal development, marine pollution, overexploitation of marine resources, and inland pollution, distance-based threat surfaces were developed from 12 representative stressors. These included cities, settlements, airports and military bases, population density, mines, tourist resorts, ports, oil tanks and wells, shipping routes, and areas where blast fishing or fishing using poisons is known to occur.

Additionally, a watershed-based model was used to estimate potential erosion within the watershed to produce an estimate of areas potentially threatened by inland pollution and sedimentation. The 13 threat surfaces were integrated with data on coral reef locations, resulting in a global classification of potential threat to coral reefs.