Port areas are socio-ecosystems impacted by chronic mixture pollution. Some marine species benefit from living there and may be studied to define the ecological state of such environments. In this study, the risks of chronic chemical contamination and its consequences on three marine molluscs were evaluated in North Corsica (France) port areas. Mediterranean mussel Mytilus galloprovincialis, tubular sea cucumber Holothuria tubulosa and Mediterranean limpet Patella sp. were sampled in three port areas and a reference location. A set of biomarkers was analysed to evaluate oxidative stress, detoxification, energetic metabolism, neurotoxicity, immunity and bioaccumulation (metallic trace elements and organic pollutants). The objectives were to assess pollution-induced effects in organisms, to determine the best bioindicator species for the selected locations and to validate a “pool” sampling technique (when the analysis is done on a single pool of samples and not on individual samples). The results validate the sampling techniques as “pool” for management purposes. St-Florent was demonstrated as the most contaminated location. All the other locations present a low contamination, below the recommended threshold values (for metallic trace elements and organic pollutants). Finally, the limpet appears to be the best bioindicator for the selected locations. Mussel and sea cucumber are inappropriate due to their absence in this oligotrophic region and the lack of responses observed, respectively.