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The Taranto basin is a shallow water marine system in the South of Italy characterized by the presence of a lagoon environment together with a semi-enclosed bay connected to the Ionian Sea. This marine system experienced over the last few decades strong biochemical pollution and environmental degradation, and it is considered a hotspot study site for economic, ecological and scientific reasons. The aim of this study was to examine, on an annual temporal scale and with high spatial resolution, the main hydrodynamical processes and transport scales of the system by means of a 3D finite element numerical model application, adopting the most realistic forcing available. The model allowed us to assess the role played by baroclinic terms in the basin circulation, describing its estuarine nature. In particular, the main features of water circulation, salinity and temperature distribution, water renewal time and bottom stress were investigated. Our results allowed us to equate this system dynamic to that of a weakly stratified estuary, identifying the main driving sources of this mechanism. The vertical stratification over the whole year was proved to be stable, leading to a dual circulation flowing out on the surface, mainly through Porta Napoli channel, and inflowing on the bottom mainly through Navigabile channel. This process was responsible also for the renewal time faster on the bottom of the Mar Piccolo basin than the surface. Due to the great importance of the Taranto basin for what concerns sediment pollution, also the effect of currents in terms of bottom stress was investigated, leading to the conclusion that only in the inlets area the values of bottom stress can be high enough to cause erosion.