The circulation and salt balance in the Albemarle-Pamlico Sound (APS) are investigated using a 3D hydrodynamic model. Although stratification is weak, the mean flow features a two-layer gravitational circulation. At the seasonal time scale, the circulation is driven by seasonally shifting prevailing winds but also affected by the horizontal density gradients generated by geographically separated sources of freshwater and saline water. The wind-driven circulation in the northern Pamlico Sound shows a laterally sheared flow and is determined by the balance between wind stress and barotropic pressure gradient. In contrast, the circulation in the southern basin shows a vertically sheared flow and is affected by both barotropic and baroclinic pressure gradients. The salt budget in APS is controlled by river flows and salt exchanges through the inlets. The salt flux due to estuarine shear flows is much weaker than that due to tidal pumping and subtidal wind-driven barotropic transport.