The Bosporus Strait, connecting the Black Sea and the Marmara Sea in Turkey, is an example of a hydrodynamically complex strait. The Strait features a multi-layered (typically two-layer) flow system and is an example of (nearly) non-tidal exchange flow. A comprehensive measurement program including long- and short-term flow velocity, water level (near both entrances of the waterway), salinity, temperature, meteorological parameters (wind speed, wind direction, and atmospheric pressures at both entrances), and discharges of the Danube River were analyzed for the period between October 2004 and October 2005. The results show high variability in the layer velocities and salinities both temporally and spatially, and the typical two-layered current structure could be sustained for water level differences (the Black Sea minus the Marmara Sea) between zero and +45 cm. However, unidirectional flow, either northward or southward, is found at times, mostly in the fall and winter due to the severe meteorological (especially wind) conditions. The river inflow to the Black Sea is a strong control on the water level in the Bosphorus Strait—and, therefore, on the current structure—during the springtime and there is around a one-month phase lag between the peak river discharges and the peak water level increase in the strait. The relationship between the water level difference of the strait and the flow properties (thicknesses and flow rates) of both layers was also quantified from the cross-sectional current measurements. The velocity structures show both high qualitative and quantitative variability between the main channel and the side slopes of the cross-sections, and taking profile measurements on the slope without cross-sectional data may give a misleading assessment of the flow structure at the point of interest. There is strong mixing between the two layers throughout the strait causing a variation of 4–5 in the salinity of both layers between the two entrances. The non-dimensional flow rate calculation showed that the maximum exchange through the strait occurred for Composite Froude numbers (G2) of around unity.