The Golden Horn estuary (GH) is a historic inlet in the northwest direction of the Bosphorus. It is a unique region that has valuable biological resources and provides living space for a wide variety of organisms. The GH suffers symptoms of poor circulation because of low river discharges upstream. Mixing by tidal or wind stress is also negligible in the estuary. Water exchange via the Bosphorus is the main factor that controls the circulation. In this study, a three-dimensional (3D) hydrodynamic model was set up and calibrated to predict the exchange flows between the waters of the Bosphorus and the eastern part of the GH. The numerical model was simulated for 2 months, January and August, which correspond to the extreme and gentle flow regimes, respectively. The mean negative and positive exchange flows were calculated. In addition, the influence of various driving forces on GH circulation was investigated using the calibrated 3D hydrodynamic model. The results show that the difference in water-surface elevation between the Marmara Sea and the Black Sea and the density-driven circulation account for almost 80% of the exchange flows in the GH. An attempt to estimate the residence time (tau) characteristics in the GH was also made using a 3D numerical model and a simplified box model, and the results were compared.