Australian reef flats on the Cocos (Keeling) Islands atoll, Indian Ocean; Warraber Reef, Torres Strait; and Lady Elliot Island, Great Barrier Reef vary greatly in morphology (width, elevation) and hydrodynamic setting (wave and tidal regime). This study describes results from detailed wave and current measurements, under nonstorm conditions, along five reef flat transects on these reef systems and examines implications for surface geomorphic processes. Results show that wave frequency and transformation varies between reefs in a consistent manner dependent on tidal elevation, reef elevation, and reef width. A nondimensional reef energy window index (Ψ) is developed that incorporates these critical factors (water depth at spring high tide and reef width). A statistically significant relation (95% confidence interval) between Ψ and the proportion of time that wave energy propagates across reefs illustrates the index ability to characterise the wave process regime of reef flats and provide a physically meaningful descriptor of the efficacy of geomorphic processes on reefs. High values of Ψ indicate narrow and low-elevation reef flats, which are exposed to high wave energy and are geomorphically active. Low values reflect wide and high-elevation reef flats associated with less active wave and geomorphic processes. Results show that while incident energy is undoubtedly an important factor for reef geomorphology, the nature of wave modification across reef flats is equally important in governing levels of geomorphic activity that control development of surface geomorphic features on reef platforms.