The availability of quantitative long term datasets on the phytobenthic assemblages of the Mar Piccolo of Taranto (southern Italy, Mediterranean Sea), a lagoon like semi-enclosed coastal basin included in the Italian LTER network, enabled careful analysis of changes occurring in the structure of the community over about thirty years. The total number of taxa differed over the years. Thirteen non-indigenous species in total were found, their number varied over the years, reaching its highest value in 2017. The dominant taxa differed over the years. The number of species in each taxonomic division also varied. In addition to the centuries-old exploitation of its biotic resources, mainly molluscs, the basin has been subject for a long time to a range of anthropogenic driving forces linked to urbanisation, shipbuilding, agriculture and military activities, which have caused chemical and biological pollution, eutrophication and habitat destruction. It may therefore be assumed that these changes were closely related to human activities. Indeed, it was observed that the reduction of only one of these forces, i.e. urban sewage discharge, triggered the recovery of phytobenthos. Therefore, it may be assumed that if the anthropogenic pressure on the Mar Piccolo was eased, it could once again become the paradisiacal place it was held to be in ancient times.