The Marmara Sea is now the recipient of a large number of wastewater discharges from land-based sources. At the same time, it is in direct exchange both with The Black Sea and The Mediterranean. A correct and efficient wastewater management programme with nutrient removal may be acceptable if it can effectively reduce the pollution in The Marmara Sea. This can only be evaluated by means of a comparative evaluation of the relevant pollutant loads originating from the land-based sources in the coastal zone and from the adjacent seas. This paper evaluates significant quality parameters related to the Black Sea – The Bosphorus – The Marmara Sea system, quantifies the pollution exchange between The Marmara Sea and The Black Sea and provides a critical appraisal of the effect of The Black Sea on the pollution in The Marmara in comparison with land-based sources.