Wave measurements at Margarita Reef in southwestern Puerto Rico show that wave height decreases as waves travel across the forereef and into the backreef. Wave spectra reveal the presence of two wave trains impinging on the reef during the study: trade-wind waves and locally generated seas. Significant wave height calculated from the spectra show an average reduction of 19.5% from 20- to 10-m isobaths and 26% from 20- to 5-m isobaths. The significant wave height decreases an average of 82% for waves traveling across the reef crest and into the backreef. Wave-energy reduction is 35% from 20- to 10-m isobaths and 45% from 20- to 5-m isobaths. Energy loss across the reef crest is 97% which translates into the formation of strong across-the-reef currents capable of moving coarse sediment. Refraction diagrams of waves impinging on the reef from the SE provide a display of wave energy distribution around the reef. The transmission coefficients calculated for trade-wind waves and locally generated seas have means of 18% and 39%, respectively. A wave height model with negligible energy dissipation, produces wave height estimates that are, in general, within the ±15% error bands. Results of wave-energy changes from this study were applied to waves representative of hurricane conditions at the reef. Aerial photographs of the reef before and after the passage of hurricanes were compared to assess the reef changes. Changes observed in the photographs are interpreted as products of sediment transport by hurricane-generated waves. The patterns of change agree with the refraction diagrams suggesting that waves were the main agents of change at margarita Reef during severe storms.