A three-dimensional, eddy-permitting ocean circulation model with implemented bottom boundary layer model and flux-corrected transport scheme is used to calculate the pathways and ages of various water masses in the Baltic Sea. The agreement between simulated and observed temperature and salinity profiles of the period 1980-2004 is satisfactory. Especially the renewal of the deep water in the Baltic proper by gravity-driven dense bottom flows is better simulated than in previous versions of the model. Based upon these model results details of the mean circulation are analyzed. For instance, it is found that after the major Baltic inflow in January 2003 saline water passing the Slupsk Furrow flows directly towards northeast along the eastern slope of the Hoburg Channel. However, after the baroclinic summer inflow in August/September 2002 the deep water flow spreads along the southwestern slope of the Gdansk Basin. Further, the model results show that the patterns of mean vertical advective fluxes across the halocline that close the large-scale vertical circulation are rather patchy. Mainly within distinct areas are particles of the saline inflow water advected vertically from the deep water into the surface layer. To analyze the time scales of the circulation mean ages of various water masses are calculated. It is found that at the sea surface of the Bornholm Basin, Gotland Basin, Bothnian Sea, and Bothnian Bay the mean ages associated to inflowing water from Kattegat amount to 26-30, 28-34, 34-38, and 38-42 years, respectively. Largest mean sea surface ages of more than 30 years associated to the freshwater of the rivers are found in the central Gotland Basin and Belt Sea. At the bottom the mean ages are largest in the western Gotland Basin and amount to more than 36 years. In the Baltic proper vertical gradients of ages associated to the freshwater inflow are smaller than in the case of inflowing saltwater from Kattegat indicating an efficient recirculation of freshwater in the Baltic Sea. (C) 2007 Elsevier Ltd. All rights reserved.