The spatial extent over which meadows of submerged aquatic vegetation, such as seagrass, have an ecological and environmental influence is tightly limited by the exchange of water across canopy boundaries. In coastal environments, the process of vertical mixing can govern this material exchange, particularly when mean currents are weak. Despite a recently improved understanding of vertical mixing in steady canopy flows, a framework that can predict mixing in wave-dominated canopy flows is still lacking. Accordingly, an extensive laboratory investigation was conducted to characterize the rate of vertical mixing in wave-dominated flows through measurement of the vertical turbulent diffusivity (Dt,z) of an injected dye sheet. A simple model of coastal canopies, an array of wooden dowels of variable packing density, was subjected to waves with a wide and realistic range of height and period. Vertical mixing across the top of a submerged canopy is shown to be driven by both the shear layer that forms at the top of the canopy and wake turbulence generated by canopy stems. By allowing for an additive contribution from these two processes, we present a predictive formulation for the rate of vertical mixing in coastal canopies across a range of wave and canopy conditions. The rate of vertical mixing, and the dominant mixing mechanism, is highly dependent upon a Keulegan–Carpenter number (KC) that represents the ratio of the particle excursion length to the length scale that defines the canopy drag. This study enables a significantly enhanced predictive capability for the residence time of ecologically and environmentally significant species within coastal canopies.