The straits connecting two large water bodies show very strong and highly stratified currents related to meteorological, morphological, and hydrodynamic conditions. The Bosphorus is one such strait, connecting the Black Sea and the Sea of Marmara. In general, there is a two-layer current system in the strait. The southward barotropic flow is driven by the sea-level difference between these two seas, with the Black Sea having the higher level. The northward baroclinic flow, however, is driven by the difference in density (which is predominantly governed by salinity) between the Black Sea and the Sea of Marmara. In this study, the effect of the duration of a given barotropic forcing on the Bosphorus current structure was modeled by using a three-dimensional hydrodynamic modeling approach. The approach is based on a number of unstructured flexible meshes and uses a finite volume solution technique. These meshes are based on linear triangular elements. Using k-epsilon turbulence and a hydrostatic pressure assumption, the same magnitude of forcing was modeled for five different durations. The model results and measurements show that in the first four cases, which were of shorter duration, one-layered flow dominated the whole channel, while in the fifth case, a two-layer flow persisted.