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As part of a five years monitoring project "Water Quality Monitoring of the Strait of Istanbul", February-December 1999 nutrient dynamics of the Black Sea-the Sea of Marmara transect are studied to evaluate the effect of discharges given by deep disposals. Through a one-year study, upper layer nutrient concentrations were generally under the effect of northwestern-shelf Black Sea originated waters. This effect was strictly observed in July, when the upper layer flow was the thickest. On the other hand, partly in November but especially in December the northwestern-shelf Black Sea originated water flow was a minimum resulting in similar concentrations in both layers. Nutrient fluctuations also affected the chlorophyll a and POC concentrations as parameters of productivity. The nutrient concentrations decreased with the effect of spring bloom and highest chlorophyll a values were detected in November at Strait stations that did not match to the Sea of Marmara values. This fact represents the time-scale difference between the Black Sea and the Sea of Marmara. On the contrary, high nutrient concentrations in the lower layer (especially inorganic phosphate), and therefore low N:P ratios reflect the effect of deep discharge. Vertical mixing caused by meteorological conditions of the shallow station (M3) under the effect of surface discharges resulted in homogenous distribution of nutrients. Nutrient concentrations of the stations affected by deep discharge showed that the two-layer stratification of the system did not permit the discharge mix to the upper layer.