Very high resolution (VHR) airborne data enable detection and physical measurements of individual coral reef colonies. The bathymetric LiDAR system, as an active remote sensing technique, accurately computes the coral reef ecosystem’s elevation and derived morphometrics using a single green wavelength at the decimetre scale over 1-to-100 km2 areas. A passive multispectral camera mounted on an airborne drone can build a blue-green-red (BGR) orthorectified mosaic and a photogrammetry-processed digital elevation model at the centimetre scale over 0.01-to-0.1 km2 areas. A combination of these technologies is used for the first time here to map coral reef patches. Airborne drone BGR values serve to calibrate airborne bathymetric LiDAR elevation and intensity data. An index of ecological state is then mapped at the scale of coral colonies through an artificial neural network (ANN). The model was developed over a small area (0.01 km2) in the lagoon of Moorea Island (French Polynesia) at VHR (0.0078 m) and then extended to the whole lagoon (46.83 km2) at HR (2 m). The ANN was first calibrated with 273 samples to determine an index of coral state through LiDAR-based predictors, then the model was validated by means of 137 samples, reaching a satisfactory performance (r = 0.82).