The Mar Piccolo of Taranto, classified as a 'Site of National Interest' (SIN), is a semi-enclosed basin divided into two inlets with lagoon features and sea influences, seriously affected by anthropic activities. In the framework of the RITMARE project, a study has been carried out to evaluate the functionality of this ecosystem. As part of this work, measurements of the water abiotic parameters were performed in order to assess the physical-chemical features of this area after the activation, in the last decade, of treatment plants for various urban and industrial dumping. Seawater intrusions and continental inputs, as well as several submarine freshwater springs, clearly affect physical-chemical characteristics of the water column in the two inlets. This finding suggests that small-scale patterns in water circulation have the potential to influence the chemical properties of the seawater. The comparison with a 20-year dataset reveals a drastic decrease in nutrient concentrations after the year 2000, validating the functionality of the treatment plants. The reduction of nutrient inputs into the basin (up to -90 % in the first inlet characterized by lower hydraulic residence time) has changed the biogeochemical characteristics of the Mar Piccolo from being relatively eutrophic to moderately oligotrophic.