In the framework of climate change, the increase in ocean heat wave frequency is expected to impact marine life. Large-scale positive temperature anomalies already occurred in the northwestern Mediterranean Sea in 1999, 2003 and 2006. These anomalies were associated with mass mortality events of macrobenthic species in coastal areas (0–40 m in depth). The anomalies were particularly severe in 1999 and 2003 when thousands of kilometres of coasts and about 30 species were affected. The aim of this study was to develop a methodology to assess the current risk of mass mortality associated with temperature increase along NW Mediterranean continental coasts. A 3D regional ocean model was used to obtain the temperature conditions for the period 2001–2010, for which the model outputs were validated by comparing them with in situ observations in affected areas. The model was globally satisfactory, although extremes were underestimated and required correction. Combined with information on the thermo-tolerance of a key species (the red gorgonian P. clavata) as well as its spatial distribution, the modelled temperature conditions were then used to assess the risk of mass mortality associated with thermal stress for the first time. Most of the known areas of observed mass mortality were found using the model, although the degree of risk in certain areas was underestimated. Using climatic IPCC scenarios, the methodology could be applied to explore the impacts of expected climate change in the NW Mediterranean. This is a key issue for the development of sound management and conservation plans to protect Mediterranean marine biodiversity in the face of climate change.