In April 2006, a large-scale hyperspectral aerial survey was conducted over the Ningaloo Marine Park, capturing spectral signatures of the lagoon with spatial resolution of approximately 3.5m. By incorporating sophisticated models that invert the spectral signatures, it is possible to simultaneously retrieve water depth and key benthic cover types (e.g. sediment, vegetation and coral) from the hyperspectral imagery. The Remote Sensing and Satellite Research Group (RSSRG) at Curtin University processed this large dataset at the iVEC supercomputing facility to produce high-resolution bathymetry and benthic cover maps over the whole of the Ningaloo Marine Park (< 20m water depth). The image-derived bathymetry products have been validated with echo sounder measurements acquired during the flight campaign and with historical acoustic bathymetry. The results indicate that the bathymetry is accurate to within ± 20cm at shallow depths up to 5m and within ± 40cm for depths ranging from 5m to 12m.