Long-term data obtained in the Turkish Strait System (TSS) including the Sea of Marmara, the Dardanelles and Bosphorus straits, during 1990-2000, have permitted us to calculate seasonal and annual fluxes of water and nutrients (nitrate, phosphate) exchanged between the Aegean and Black Seas through the TSS. Two-layer flow regimes in the TSS introduce the brackish waters of the Black Sea into the Aegean basin of the northeastern Mediterranean throughout the year. A counter flow in the TSS carries the salty Mediterranean water into the Black Sea via the Marmara deep basin. The annual volume influx from the Black Sea to the Marmara upper layer is nearly two-fold the salty water exported from the Marmara to the Black Sea via the Bosphorus underflow. The brackish Black Sea inflow is relatively rich in nitrate and phosphate in winter, decreasing to the lowest levels in late summer and autumn. Biologically labile nutrients of Black Sea origin are utilized in photosynthetic processes in the Marmara Sea and are partly exported to the Marmara lower layer. Eventually, the brackish Black Sea waters reach the Dardanelles Strait, with modified bio-chemical properties. On the other hand, the salty Mediterranean waters with low concentrations of nutrients enter the Marmara deep basin. During threir 6-7 year sojourn in the Marmara basin, the salty waters become enriched in nitrate (DIN) and phosphate (DIP), due to oxidation of planktonic particles sinking from the Marmara surface layer. The annual nutrient inputs from the Black Sea to the Marmara basin were estimated as 8.17x108 moles of DIN and 4.25x107 moles of DIP, which are much less than the importation from the Marmara lower layer via the Bosphorus undercurrent. The salty Aegean water introduces nearly 6.13x108 moles of DIN and 2.79x107 moles of DIP into the Marmara lower layer. The estimated DIP outflux from the Aegean Sea is nearly 2 times less than the importation from the Marmara Sea via the Dardanelles Strait.