In coastal semi-enclosed basins the knowledge about cleaning capacity of the system, related to the water transport and dilution process, can be crucial to decision makers in order of an aware management. This work aims to investigate the three-dimensional character of these transport time scales in the Taranto Seas (Apulia, Italy), through the application of a finite elements numerical model SHYFEM. In particular, a new Lagrangian module has been created in order to follow the 3D particles motion, computing three-dimensional Water Transit Time (WTT) and comparing it with the Water Renewal Time (WRT) of the basin. The results, summarized in the Trapping Index (TI) variable, allowed to identify the retention areas of the Taranto Seas both on the surface and on the bottom of the system.