Coral bleaching is often characterized by high spatial variation across reef systems. Using a field survey and manipulative experiment, we tested whether the physical structure of coral reefs modifies environmental conditions that, in turn, influence spatial variation in bleaching in 3 scleractinian corals, Pocillopora verrucosa, Acropora elseyi, and Porites rus. Corals inhabit mainly the hard-bottom seafloor, or dead or partially dead coral heads ('bommies'). Bommies (0.10 to 3.0 m tall) position corals at different water depths and expose them to differences in light, temperature, hydrodynamics, and sedimentation, factors that can influence patterns of bleaching. We conducted our Study in association with a 14 d warming event that caused bleaching in lagoons of Moorea, French Polynesia. Bleaching in naturally occurring colonies of Pocillopora spp. and Acopora spp. was greater on the seafloor (0 m tall) than on short (0.35 to 0.40 m tall) and tall bommies (1.0 to 1.2 m tall). Bleaching in P. verrucosa and A. elseyi transplanted to reef structures in the experiment generally decreased with increasing reef height (seafloor > short bommies > tall bommies). P. rus did not bleach under any conditions observed. Regression analyses revealed that reef structure controlled current speed and sedimentation at the microhabitat scale (from centimeters to meters), and that these factors regulated bleaching and mortality in P. verrucosa and A. elseyi. Our results imply that the physical structure of shallow water reef habitat influences the performance of coral colonies by modifying environmental stress, and that accounting for this structure is important in managing coral reef systems.