Quantification of the turbulent kinetic energy dissipation rate in the water column, , is very important for assessing nutrient uptake rates of corals and therefore the health of coral reef lagoon systems. However, the availability of such data is limited. Recently, at Lady Elliot Island (LEI), Australia, we showed that there was a strong correlation between in situ measurements of surface-wave energy dissipation and ∈. Previously, Reineman et al. (2009), we showed that a small airborne scanning lidar system could measure the surface wavefield remotely. Here we present measurements demonstrating the use of the same airborne lidar to remotely measure surface wave energy fluxes and dissipation and thereby estimate ∈ in the LEI reef-lagoon system. The wave energy flux and wave dissipation rate across the fore reef and into the lagoon are determined from the airborne measurements of the wavefield. Using these techniques, observed spatial profiles of energy flux and wave energy dissipation rates over the LEI reef-lagoon system are presented. The results show that the high lidar backscatter intensity and point density coming from the high reflectivity of the foam from depth-limited breaking waves coincides with the high wave-energy dissipation rates. Good correlations between the airborne measurements and in situ observations demonstrate that it is feasible to apply airborne lidar systems for large-scale, long-term studies in monitoring important physical processes in coral reef environments. When added to other airborne techniques, the opportunities for efficient monitoring of large reef systems may be expanded significantly.