The Bosphorus, located at the junction of Asia and Europe, controls the transports of water, material, and energy between the Black Sea (BS) and the Mediterranean Sea. The Canal Istanbul (CI), planned by Republic of Turkey (TR), is a gigantic project which bisects the current European side of Istanbul, thus forming a secondary waterway parallel to the existing natural channel of the Bosphorus. The environmental impact of this project has been a major concern since the very beginning. To address this concern, a 3D hydrodynamic modeling study is carried out to investigate the impact of CI on the hydrodynamics and salinity of the northern Sea of Marmara (SM) by using the route and cross-section (CS) of canal, which was recently made public by the TR. An extensive set of model calibration is performed in a model where only the Bosphorus Strait links the Black Sea and Marmara Sea. Once the calibration process is completed, the future canal is added into the grid and new simulations are performed to analyze the influence of CI on hydrodynamics and salinities in the SM. It was found that the shallow water depth of CI is the limiting factor constraining the two-layer flow. Thus the vertical current structure of CI appears mostly as one-layer flow from the BS to the SM. One-layer flow from the SM toward the BS is rarely observed. In such cases, strong northerly storms caused water level setup at the SM and set down at the BS. Adding the CI in the model is responsible for a salinity decrease of 1 ppt in the surface layer of SM. The salinity difference between the two models decreases gradually with the depth and it diminishes at the depth of 25 m.