Turkey has announced its plan to construct a new waterway, Canal Istanbul, parallel to the Bosphorus. In this study, the influence of Canal Istanbul on salinity distribution in the northern Marmara Sea is investigated using a previously calibrated 3D hydrodynamic and salinity model. Moreover, the salinity field of the canal and its propagation are examined based on various meteorological cases. Finally, the flow structure of the canal is determined. It is calculated that at the southern end of the canal, mainly unidirectional flow (from the Black Sea to the Marmara Sea) occurs during 68% of the simulation period. A two-layer flow is seen only 28% of the time with a weak lower layer flow, whereas this value decreases to 4% at the north end of the canal. In the southward direction (to the Marmara Sea), velocities higher than 1.5 m/s are rarely observed along the canal. The average surface salinity difference in the northern Marmara Sea due to the construction of the canal is calculated to be smaller than 0.50 ppt. The salinity difference gradually diminishes as water depth increases and after 25 m (from the surface) almost no difference is observed.