The Cassidaigne canyon is one of the two canyons (together with Lacaze-Duthiers) of the French Mediterranean coast in which cold-water corals have settled and formed large colonies, providing a structural habitat for other species. Nevertheless, the communities settled in the Cassidaigne canyon are physically impacted by discharges of bauxite residues. New information on the distribution of the species Madrepora oculata and the associated species diversity in Cassidaigne canyon was provided by videos and photos acquired in 2013. An area investigated at 515 m depth harbored a high density of small colonies of M. oculata. The water column structure of the area was described by using a CTD transect deployed along the axis of the canyon. High resolution (10 m and 2 m) bathymetric data were collected in the Cassidaigne canyon in 2010 and 2014. Seafloor characteristics were derived from the 10 m resolution bathymetric data. Data on local hydrodynamic conditions in the first 10 m above the seafloor were produced by applying the MARS3D hydrodynamic model in the Cassidaigne canyon at a horizontal resolution of 80 m (CASCANS model configuration). These environmental datasets combined with the geographic coordinates of the known occurrences of dense M. oculata colonies in the canyon allowed establishing a model using the MaxEnt software package to predict the habitat distribution in terms of probability of occurrence. According to the water mass analysis, M. oculata habitats are mainly located in the layer of the Intermediate waters originating from the Eastern Mediterranean Basin. A high concentration of suspended sediment due to the bauxite residues expelled into the canyon was observed in the axis of the canyon where we measured 1 NTU (2.5 mg/l) at 100 m above the bottom while concentrations were even higher (2 NTU; 5 mg/l) closer to the bottom. The habitat suitability model indicates that the living conditions of M. oculata can be found in areas of the Cassidaigne canyon where the substratum shows irregularities, slopes and topographic highs. Concerning environmental variables resulting from the hydrodynamic model, temperature and high current velocities were identified as explanatory factors of the distribution of M. oculata. Suitable areas for M. oculata habitat settlement were mapped at the scale of the canyon. This study gathers multiple disciplines combined to consider a submarine canyon as a global functioning system and is an approach intended to promote the management of sensitive ecosystems in complex topographic features such as canyons.