It has been shown that one of the properties of climatic circulation in the Gulf of Trieste (Gulf) is the input current near the sea floor in all seasons (Malačič and Petelin 2009). The circulation in the Gulf is very much dependent on the circulation of the northern Adriatic (Zavatarelli and Pinardi 2003), (Figure, top row for the domains of interest). Climatic circulation of the Gulf (Figure, bottom left) has been also applied in the study of the spread of cooled sea-water that is meant to heat the liquefied natural gas (LNG), stored in the planned LNG terminals at two locations on the Italian side of the Gulf (Malačič et al. 2008). Climatic and particularly synoptic circulation in small (5 km) wide open bays (Bays of Piran, Koper and Muggia) that face the Gulf (Figure, top), are not yet known. The circulation is certainly very much dependent on the circulation of the Gulf and on the topography of the bays, where the curvature radius of promontories, which confine these bays, is important as well (Valle-Levinson and Moraga-Opazo 2006). The transport of sediments in the northern Adriatic depends on circulation. The re-suspension, however, depends on the vertical shear of bottom currents and also on surface waves (Wang et al. 2007). However, in the inside, closed part of shallow bays maritime traffic may be the dominant agent for re-suspension, as indicated by the first measurements of turbidity in the Bay of Koper (Malačič et al. 2010). It looks like ship maneuvering adds to turbidity, thus also to re-suspension, more than surface waves and currents together in stormy weather. The applied project is motivated by the need to know how, where and when the re-suspended sediment in the Bay of Koper, which has naturally elevated concentrations of nickel (Malačič et al. 2010), travels around and out of the Bay. The same information about the cross-border travel of re-suspended sediment, which is lifted up in the central and northern part of the Gulf, and is contaminated by mercury (Covelli et al. 2001), is important as well. The information obtained will accomplish two things: First, it will contribute to the management of the Bays of Koper and Piran and will estimate the effects of maritime traffic on sediment, consequently on benthic organisms, due to the enlargement of the capacity of the Port of Koper. Second, it will be an added value in the evaluation of the cross-border influences of gas terminals, which are in the serious planning stage on the Italian side, on the marine environment. The legal ground for this investigation lies in a recent ‘Decision’ of the European Commission (C(2010) 5956 (Anon. 2010), which defines the criteria and methodological standards for the good environmental status of marine waters. Descriptor 7 advises that permanent alteration of hydrographical conditions do not adversely affect marine ecosystems’ and that ‘a case by case approach is necessary to assess the impact of activities. Tools such as environmental impact assessment may contribute to evaluate and assess the extent and the cumulative aspects of impacts from such activities’ and ‘…that such tools provide for adequate elements to assess potential impacts on the marine environment, including transboundary considerations.’ The project will reveal the circulation characteristics of wide open bays, like the Bays of Piran, Koper and Muggia by using two numerical models of different architecture. It will estimate the residence time of water mass inside bays and relate it to the spread of pollutants released from different locations. It will study the re-suspension of sediments due to currents and waves and the spread of sediments due to currents. However, it will be focused on the re-suspension of sediments due to maritime traffic by the state-of-the-art measurements and numerical models, which have not yet been applied for this purpose.