This paper presents the results of a numerical study on the potential impact of Canal Istanbul on the two-layer flow system in the Bosphorus, the strait connecting the Black Sea and the Marmara Sea. (Canal Istanbul is a planned artificial waterway connecting the Black Sea to the Sea of Marmara, located to the West of the Bosphorus, ca. 30 km from the Bosphorus in the north and ca. 15 km in the south.) The numerical model is a three-dimensional model incorporated with the large Eddy simulation (LES) model for the horizontal turbulence closure and a modified mixing-length model for the vertical turbulence closure. It was found that there is a one-directional, single-layer flow in Canal Istanbul (the flow direction being from the Black Sea to the Marmara Sea), in contrast to the two-layer flow system in the Bosphorus. The reverse flow in Canal Istanbul is essentially nil because the design depth of the canal, 21 m, is not large enough to accommodate the latter flow. The flow rate in the canal was found to be 6.4 × 10³ m³/s. It was also found that the head difference between the Black Sea and the Marmara Sea, the main driver for the flow in the upper layer of the Bosphorus, does not remain unchanged; it decreases to 25.7 cm, a value notably smaller than what might be called the precanal value, 33 cm. It was found that, with the introduction of the canal, the length-averaged flow rates changed from 18.55 × 10³ to 14.95 × 10³ m³/s in the upper layer and from 6.55 × 10³ to 9.35 × 10³ m³/s in the lower layer of the Bosphorus for the mean flow conditions. (The length-averaged flow rate is defined as the average between the flow rate at the north end of the Bosphorus and that at the south end of the Bosphorus.) It was also found that while there exists a net amount of transfer of water from the lower layer into the upper layer across the density interface in the precanal situation, the opposite is true in the postcanal situation in that there exists a net amount of transfer of water, this time, from the upper layer into the lower layer, the total amount of water transferred from the upper layer into the lower layer being 0.9 × 10³ m³/s (cf., 2.9 × 10³ m³/s transfer of water from the lower layer into the upper layer in the precanal situation). It was further found that, in the postcanal scenario, the total amount of the Black Sea water flowing into the Marmara Sea increases by 4.5% with respect to that corresponding to the precanal situation, meaning that Canal Istanbul alone will carry 30.6% of the total Black Sea water flowing into the Marmara Sea, an issue that has important consequences for the pollution of the Marmara Sea. The paper discusses other issues as well with regard to the impact of Canal Istanbul on the flow through the Bosphorus.