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Boka Kotorska Bay, located in the southeastern Adriatic Sea along the Montenegro coastline, is a complex morphological structure, consisting of three embayments. They are connected and interact with the sea through narrow straits and the bay can be considered one of the main freshwater inputs into the southern Adriatic Sea. In the framework of the ADRICOSM-STAR project, a hydrodynamical model of this region provided results that are compared with CTD data and hydrodynamic scenarios are discussed for the bay. A finite element coastal model nested in a finite difference model that runs on the Adriatic Sea has been used to reproduce the complex morphology of the bay. Hydrodynamic modeling allows studying the main characteristics of this bay, identifying it as a Region of Freshwater Influence (ROFI). The freshwater input coming from the numerous sources present in the bays can strongly modify temperature, salinity and current patterns. The computation of the buoyancy ratio of the thermal and haline buoyancy flux showed that the Kotor and Morinj Bays experience a major effect of surface heating in summer, while the rest of the bay seems to be mostly affected by freshwater influence from precipitation and river discharge. An average estuarine situation is seen, presenting a surface outflow and a bottom inflow of water. Specific hydrodynamic processes can be detected in the channels that connect the different sub-basins of the Boka Kotorska Bay. Moreover, the computation of the Kelvin number in correspondence of the internal straits suggests classifying the Kotor and Morinj Bays differently from the outermost areas. The innermost Kotor and Morinj Bays, generally exchange little water with the sea and they have high values of residence times. However, their fresh water springs and rivers have the highest discharges that can change abruptly the picture with increase of the total water exchange between the bay and the sea.