AbstractThe Turkish Straits System (TSS) is a region of intense mixing between the Black Sea and the Mediterranean Sea exerting crucial control on the water & substance exchange through the Bosphorus and Dardanelles straits between these two sea basins. A waterway project, namely the Canal Istanbul, was proposed to be built within this system parallel to the Bosphorus. Even tough environmental impacts of the project have been of concern, a few studies that address these scientific and public concerns under the light of scientific methods are available. In order to fill this gap in the literature, a three-dimensional hydrodynamic model with realistic forcing has been set up for long-term integration. The study includes simulating of two scenarios for the adjacent basins; (i) existing configuration of the TSS, and (ii) the proposed extension with the recent planned route of Canal Istanbul that was added to the validated model. The results reveals that the canal project would increase the exchange flow between the Black Sea and the Mediterranean Sea in both directions while causing slight changes in temperature & salinity along the TSS. Findings of this study can be used in further research that would analyze the impacts of the proposed Canal Istanbul on the water quality and ecosystem of the TSS.