This study focuses on the influence of extreme hydrological events on the water quality of the Strait of Istanbul (Bosphorus), a stratified waterway, polluted by sewage outfalls and non-point sources. Monthly collected water quality parameters (nitrate + nitrite, ortho-phosphate, silicate, dissolved oxygen, total suspended solids, chlorophyll-a and fecal indicator bacteria (fecal coliform and enterococci)) were evaluated together with the hydrological data (salinity, temperature and current flow) for 1 year. Two blockage events, identified as extreme conditions, were detected during the study: a lower layer blockage in February 2003 and an upper layer blockage in October 2003.

During the lower layer blockage, the volume fluxes of the upper layer significantly increased to 28,140 m3 s− 1 and the lower layer almost stopped flowing (19 m3 s− 1). The dissolved oxidative nitrogen, ortho-phosphate and silicate inputs outflowing from the Black Sea were 117, 17.6, and 309 tons which were 3, 2, and 4 times the average daily fluxes respectively, in addition to enhancement of fecal indicator bacteria contamination in the sea surface flow.

During the upper layer blockage, the volume flux of the upper layer was 3837 m3 s− 1 and the counter flow reached 24,985 m3 s− 1 at the northern exit of the Strait of Istanbul resulting in 2.7 fold increase in the mean bottom flow. The daily exports of nutrients, total suspended solid and dissolved oxygen by the lower layer flow increased by at least 2 fold compared to the mass fluxes estimated from the seasonal/annual means of volume flux and concentrations. On the other hand, fecal indicator bacteria flux by the lower layer inflow to the Black Sea decreased by at least 2 fold compared to the mean daily flux. These results show that the material exchange between the Marmara and the Black seas becomes more important during blockage events.