This volume compiles a number of scientific papers resulting from a sustained multidisciplinary research effort of the deep-sea ecosystem in the Mediterranean Sea that started 20 years ago, which has peaked over the last few years thanks to a number of Spanish and European projects like PROMETEO, DOS MARES, REDECO, GRACCIE, HERMES, HERMIONE and PERSEUS, amongst other projects. The geographic focus of most papers is on the NW Mediterranean Sea including the Western Gulf of Lion and the North Catalan margin, with a special attention to submarine canyons, in particular Blanes and Cap de Creus canyons.This introductory article to the Progress in Oceanography special issue on ''Mediterranean deep canyons'' provides background information needed to better understand the individual papers forming the volume, comments previous reference papers related to the main topics here addressed, and finally highlights the existing relationships between atmospheric forcing, oceanographic processes, seafloor physiography, ecosystem response, and litter and chemical pollution. This article also aims at constituting a sort of glue, in terms of existing knowledge and concepts and novel findings, linking together the other twenty papers in the volume, also including some illustrative figures.The main driving ideas behind this special issue, particularly fitting to the study area of the NW Mediterranean Sea, could be summarized as follows: (i) the atmosphere and the deep-sea ecosystem are connected through oceanographic processes originating in the coastal area and the ocean surface, which get activated at the occasion of highenergy events leading to fast transfers to the deep; (ii) shelf indented submarine canyons play a