The study of the physical–chemical parameters in the Mar Piccolo of Taranto, begun since the first years of the last century. In these selected studies physical–chemical characterization of marine water and sediments were carried out in the first and second inlet of the basin. In marine water, temperature, salinity, dissolved oxygen, ammonia, nitrites, nitrates, and orthophosphates were determined. In sediments physical–chemical parameters included: water content, organic matter, total nitrogen and total phosphorous, pH, red-ox potential and grain size classification. Moreover, different micropollutants were also evaluated: heavy metals (Hg, Cd, Pb, Cr, Cu, Ni, Zn, Al V and Fe) and Arsenic, polycyclic aromatic hydrocarbons (PAHs), polychlorobiphenyls (PCBs), organochlorinated pesticides and organotin compounds. These studies demonstrate the important role of water monitoring studies in the semi-enclosed basin of the Mar Piccolo with lagoon features, characterized also by mussel farming activities. Moreover, in addition to the trophic conditions of the area, data obtained from sediments characterization allow us to evaluate the possible contaminants transfer along the food chain, in order to protect human health by consumption of seafood products