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A common technique for estimating the sea surface generation functions of spray and aerosols is the so-called flux–profile method, where fixed-height concentration measurements are used to infer fluxes at the surface by assuming a form of the concentration profile. At its simplest, this method assumes a balance between spray emission and deposition, and under these conditions the concentration profile follows a power-law shape. It is the purpose of this work to evaluate the influence of waves on this power-law theory, as well as investigate its applicability over a range of droplet sizes. Large-eddy simulations combined with Lagrangian droplet tracking are used to resolve the turbulent transport of spray droplets over moving, monochromatic waves at the lower surface. The wave age and the droplet diameter are varied, and it is found that droplets are highly influenced both by their inertia (i.e., their inability to travel exactly with fluid streamlines) and the wave-induced turbulence. Deviations of the vertical concentration profiles from the power-law theory are found at all wave ages and for large droplets. The dynamics of droplets within the wave boundary layer alter their net vertical fluxes, and as a result, estimates of surface emission based on the flux–profile method can yield significant errors. In practice, the resulting implication is that the flux–profile method may unsuitable for large droplets, and the combined effect of inertia and wave-induced turbulence is responsible for the continued spread in their surface source estimates.