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The Sea of Marmara, an intercontinental basin with two narrow and shallow straits permitting the exchange of the Mediterranean and Black Sea waters, receives 2.8×104 tons TP (total phosphorus), 2.7×105 tons TN (total nitrogen) and 1.9×106 tons TOC (total organic carbon) per year from the Black Sea inflow, from the lower layer by vertical mixing and from anthropogenic inputs of various origins including riverine discharges. The Black Sea input through the Bosphorus constitutes about 35, 64 and 77 %, respectively, of the total annual loads of TP, TN and TOC entering the Marmara surface waters. Pollution loadings from Istanbul make up a major fraction (40-65%) of the total anthropogenic discharges. The biochemical properties of the productive Marmara upper layer appear to be dominated by the inputs both from its lower layer by vertical mixing and from the Black Sea throughout the year. Pollution discharges from Istanbul have secondary importance for the nutrient and organic carbon pools of the Marmara Sea; however, the land-based chemical pollution has drastically modified the ecosystem of coastal margins and semi-enclosed bays (e.g. Golden Horn, Izmit and Gemlik) where water exchanges with the open sea are limited. Biologically labile nutrients increasingly exported from the Black Sea in the spring-early summer, are compensated by importation from the Marmara Sea through the Bosphorus underflow. The less labile dissolved organic nitrogen and carbon input from the Black Sea appears to reach as far as the Aegean basin of the Northeastern Mediterranean in 4-5 months without contributing to the net production in the Marmara Sea.