The input of industrial and domestic waste to the horizontal circulation in the Golden Horn Estuary of Marmara Sea has resulted in one of the most polluted estuaries in the past. Consequently, the dissolved oxygen concentrations in both the surface and bottom waters decreased toward to the estuary head during 1998-2005. In contrast, the total suspended solids content of the surface water decreased toward to the estuary mouth. However, construction of the operational collector system surrounding the estuary during the process of rehabilitation projects, combined with the opening of the middle pontoons of the Valide Sultan Bridge, resulted in gradually improved water quality of the estuary with a concomitant decrease in pollution. However, phytoplankton blooms and eutrophication persist especially in the innermost part of the Golden Horn in 2005. The region from the estuary mouth up to CamialtA +/- has a dynamic structure, and sufficient circulation seemingly occurs in this part of the Golden Horn.