To live successfully in wave-swept habitats, plants and animals must be able to survive, consume resources, and reproduce in the presence of incessant, variable and often unpredictable levels of water motion at a range of scales. However, there is a relatively poor understanding of water motion in natural habitats at the scales necessary to determine its potential physiological and ecological consequences. Using an historic record of hourly wind conditions, a depth profile and two rigorously tested oceanographic models, 37-years of hourly wave driven water motion were hindcast spatially on a typical subtidal coral reef platform (maximum horizontal displacement, velocity and acceleration per wave cycle). For larger waves, those likely to constitute ecological disturbances, around 95% of the wave's height that is lost over the whole reef occurs within the first 50 m of the crest. The field-validated model of spatiotemporal variation in water motion provided a framework for quantitatively predicting several physiological and ecological effects of wave motion, such as nutrient and gas fluxes and mortality rates from hydrodynamic disturbances. It also suggested a sharp ecological transition between a crest habitat in which disturbance-mediated coexistence mechanisms are important, and a flat habitat in which they are much less important.