The mussel and fish-farming impact was investigated both in pelagic and sediment environments of Mar Piccolo in Taranto. We studied the yearly distribution of microbiological indicators (heterotrophic bacteria and coliforms), in relation to physical and chemical parameters of surface water at three different sites, characterized by mussel farms, fish cages and Citro springs. The heterotrophic bacteria and Clostridium perfrigens distribution were also examined in relation to organic content and granulometry of sediments. The urban sewages affected the quality of waters of the mussel site, by increasing faecal coliforms in the entire basin during summer. In the benthonic environment the aquaculture activity increased the bio-deposition of the sediment, causing changes in the abundance and the composition (heterotrophic bacteria/clostridia ratio) of microflora. A significant increase of heterotrophic bacteria in the warm season was observed. The clostridia proved to be a good indicator of impact of organic matter because they were significantly higher in the sites than the control stations.