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Coral reefs and associated benthic habitats are heterogeneous in nature. A remote sensor designed to discriminate these environments requires a high number of narrow, properly placed bands which are not currently available in existing satellite sensors. Optical hyperspectral sensors mounted on aerial platforms seem to be appropriate for overcoming the lack of both high spectral and spatial resolution of satellite sensors. This research presents results of an innovative coral reef application by such a sensor. Using hyperspectral Airborne Imaging Spectroradiometer for Applications (AISA) Eagle data, the approach presented solves the confounding influence of water column attenuation on substrate reflectance on a per‐pixel basis. The hyperspectral imagery was used in band ratio algorithms to derive water depth and water column optical properties (e.g., absorption and backscattering coefficients). The water …