The Rade de Cherbourg (RdC), in the North Cotentin (Normandy, English Channel) is the only French coastal zone where an offshore salmon farm has been in operation over the past three decades. Our study leads to the identification of the Ecological Quality status of benthic habitats based on a one-year survey (2013–2014) underneath and near the cages as well as in non-impacted areas lying outside the influence of salmon farming. The semi-diurnal high tide regime of the Rade de Cherbourg (5 to 8 m tidal range from neap to spring tide) should prevent any significant accumulation of Organic Matter (OM) under the cages. Nevertheless, higher Total Organic Carbon (TOC) and the presence of opportunistic species at sampling stations under and near the cages indicate an impact of salmon farming on the benthic habitats. Three benthic assemblages are identified, corresponding to three sediment types with different levels of OM enrichment. The presence of several indicator species, such as the polychaete worm Capitella minima belonging to the Capitellidae, reflects the local impact of fish farming without long-term accumulation of OM in the shallow waters of the RdC. Moreover, one of the main characteristics of the macrofauna of the RdC and neighbouring zones is the current very high abundance and dominance of the tanaid Apseudopsis latreillii in diverse sediment types. Benthic indices (AMBI, M-AMBI, and BO2A) were also able to distinguish three main zones in relation to the distance to salmon cages.