A recent tsunami and an apparent increase in the frequency of severe tropical storms underscore the need to understand and predict the ecological consequences of major hydrodynamic disturbances. Reef corals provide the habitat structure that sustains the high biodiversity of tropical reefs, and thus provide the foundation for the ecosystem goods and services that are critical to many tropical societies. Here we integrate predictions from oceanographic models with engineering theory, to predict the dislodgement of benthic reef corals during hydrodynamic disturbances. This generalizes earlier work, by incorporating colonies of any shape and by explicitly examining the effects of hydrodynamic gradients on coral assemblage structure. A field test shows that this model accurately predicts changes in the mechanical vulnerability of coral colonies, and thus their size and shape, with distance from the reef crest. This work provides a general framework for understanding and predicting the effects of hydrodynamic disturbances on coral reef communities; such disturbances have a major role in determining species zonation and coexistence on coral reefs, and are critical determinants of how coral assemblages will respond to changes in the frequency and intensity of tropical storms associated with a changing climate.