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Abstract: The bathymetric LiDAR system is an airborne laser that detects sea bottom at high vertical and horizontal resolutions in shallow coastal waters. This study assesses the capabilities of the airborne bathymetric LiDAR sensor (Hawk Eye system) for coastal habitat mapping in the Oka estuary (within the Biosphere Reserve of Urdaibai, SE Bay of Biscay, northern Spain), where water conditions are moderately turbid. Three specific objectives were addressed: 1) to assess the data quality of the Hawk Eye LiDAR, both for terrestrial and subtidal zones, in terms of height measurement density, coverage, and vertical accuracy; 2) to compare bathymetric LiDAR with a ship-borne multibeam echosounder (MBES) for different bottom types and depth ranges; and 3) to test the discrimination potential of LiDAR height and reflectance information, together with multi-spectral imagery (three visible and near infrared bands), for the classification of 22 salt marsh and rocky shore habitats, covering supralittoral, intertidal and subtidal zones. The bathymetric LiDAR Hawk Eye data enabled the generation of a digital elevation model (DEM) of the Oka estuary, at 2 m of horizontal spatial resolution in the terrestrial zone (with a vertical accuracy of 0.15 m) and at 4 m within the subtidal, extending a water depth of 21 m. Data gaps occurred in 14.4% of the area surveyed with the LiDAR (13.69 km2). Comparison of the LiDAR system and the MBES showed no significant mean difference in depth. However, the Root Mean Square error of the former was high (0.84 m), especially concentrated upon rocky (0.55–1.77 m) rather than in sediment bottoms (0.38–0.62 m). The potential of LiDAR topographic variables and reflectance alone for discriminating 15 intertidal and submerged habitats was low (with overall classification accuracy between 52.4 and 65.4%). In particular, reflectance retrieved for this case study has been found to be not particularly useful for classification purposes. The combination of the LiDAR-based DEM and derived topographical features with the near infrared and visible bands has permitted the mapping of 22 supralittoral, intertidal and subtidal habitats of the Oka estuary, with high overall classification accuracies of between 84.5% and 92.1%, using the maximum likelihood algorithm. The airborne bathymetric Hawk Eye LiDAR, although somewhat limited by water turbidity and wave breaking, provides unique height information obscured from topographic LiDAR and acoustic systems, together with an improvement of the habitat mapping reliability in the complex and dynamic coastal fringe. [Copyright &y& Elsevier]