Three seasonal sampling campaigns (winter, summer before touristic period, summer after touristic period) were implemented during 2012 in three Mediterranean touristic ports: Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia). Three to five stations were sampled per port, which were part of different port sectors (leisure, fishing, passenger, cargo, shipyard). Three water and three sediment replicate samples were collected per station for analysis of nutrients, pigments and hydrocarbons. One replicate was analysed for physical parameters, heavy metals and granulometry. Five sediment replicates were collected for analysis of benthic biodiversity. Benthic organisms were sorted to the main taxonomic groups (e.g. .Annelida, Mollusca, Arthropoda, Echinodermata) and identified to species level.