Hyperspectral remote sensing inversion models utilize spectral information over optically shallow waters to retrieve optical properties of the water column, bottom depth and reflectance, with the latter used in benthic classification. Accuracy of these retrievals is dependent on the spectral endmember(s) used to model the bottom reflectance during the inversion. Without prior knowledge of these endmember(s) current approaches must iterate through a list of endmember—a computationally demanding task. To address this, a novel lookup table classification approach termed HOPE-LUT was developed for selecting the likely benthic endmembers of any hyperspectral image pixel. HOPE-LUT classifies a pixel as sand, mixture or non-sand, then the latter two are resolved into the three most likely classes. Optimization subsequently selects the class (out of the three) that generated the best fit to the remote sensing reflectance. For a coral reef case, modeling results indicate very high benthic classification accuracy (>90%) for depths less than 4 m of common coral reef benthos. These accuracies decrease substantially with increasing depth due to the loss of bottom information, especially the spectral signatures. We applied this technique to hyperspectral airborne imagery of Heron Reef, Great Barrier Reef and generated benthic habitat maps with higher classification accuracy compared to standard inversion models.