The reefs surrounding Bonaire have long been renowned for their high abundance and diversity of scleractinian corals and for their long-time status as a protected marine park. As part of a comprehensive study of the current status of Bonaire’s reefs, a quantitative benthic community survey was conducted at 7 locations across depths from 10 to 30 m in early 2008. This showed mean coral cover ranging from 23.7% ± 3.8 (SE) to 38.4% ± 4.4 (SE) on the island’s leeward shore and 1.6% ± 0.4 (SE) to 22.4% ± 3.6 (SE) on the windward shore. Percent cover of macrophytes and turf algae ranged from 41.7% ± 2.0 (SE) to 51.8% ± 3.0 (SE) on the leeward shore and 60.8% ± 4.1 (SE) to 82.7% ± 2.5 (SE) on the windward shore. Comparison of these results to earlier work from 1982 on the leeward shore and 1988 on the windward shore points to a significant, system-wide decrease in corals, increase in macroalgae and increase in the ratio of algae to corals. These observations point to significant degradation of reefs at a site often described as relatively ‘pristine’ in the Caribbean and highlight the sensitivity of coral reefs to anthropogenic and natural stresses even on well-protected islands.