Stratified flows in open channels arise as a result of density or surface level differences. If the channel is connected to a basin at one or both ends, strong winds originating from the basin cause the "wind setup" effect that increases the water level at the entrance of the channel. On the other hand, along the channel, persistent winds in the upper layer flow direction lead to an increase of the drift velocity and to a decrease in upper layer flow depth. The Istanbul Strait (Bosphorus) connecting the Black and the Marmara Seas, is characterized by a stratified flow caused by the surface level and salinity difference between these basins, consisting of a southward upper layer flow and a northward lower layer flow. Along the strait, there are three hydraulic control points; the north sill, a midway contraction reach and the south sill. Under wind effects, the northern and southern entrances of the strait behave as an estuary whereas the midway reach to the south of the contraction acts as as an open channel. In winter, when the sea level difference is relatively low, the wind setup due to southerly winds may cause a blockage and even reversal of the upper layer flow. On the other hand in spring when there is excessive river discharge, northerly winds increase the influx of Black Sea waters into the strait and may lead to a blockage of the lower layer. We claim that strong northerly winds may cause a decrease of the upper layer depth beyond the contraction and we propose a simple model for its estimation in terms of the wind and water flow speeds.