The Bosphorus Strait is a typical example of a narrow sea strait and, in general, has a two-layer flow structure. Driven by the water level difference between the Black Sea (north) and the Sea of Marmara (south), a lighter upper layer flows from north to south. A denser lower layer flow is caused by the density difference between the adjacent seas and flows in the opposite direction. In this study, the three-dimensional (3D) flow structure of the Bosphorus strait was modeled using the MIKE 3 hydrodynamic numerical code. Selecting the drag coefficient (c(f)), buoyancy parameter (c(epsilon 3)), and turbulence Prandtl number (sigma(t)) as calibration parameters, the model was calibrated using genetic algorithms with available current measurements at three different depths for one given location. The root-mean-square errors of the calibrated model were calculated to be 0.266, 0.201, and 0.163 m/s at the depths considered, respectively. The model was also validated temporally, for four different time periods and spatially, at another location in the strait. The validated models show good overall agreement with the field measurements. This paper is also relevant to determining the hydrodynamic design criteria of marine structures, and safe marine navigation in the waterway will be considered. DOI: 10.1061/(ASCE)WW.1943-5460.0000132. (C) 2012 American Society of Civil Engineers.