Eutrophication processes and changes in coastal ecosystem are determined by the coastal/open sea interactions and rates of nutrient pollution. The Cilician Basin shelf waters are affected not only by intense industrial activities and increased population, but also by complex atmosphere-sea-land interactions. There is a recognizable difference between water qualities of Mersin bay coastal and the Cilician open waters depleted in nutrients. Eutrophic conditions have developed in the eastern bay shallow waters heavily polluted by land-based inputs during the last few decades. In the present study, basic chemical parameters measured seasonally in water column during the 8 field surveys, as a part of TUBITAK project, in the period of November 2005-September 2007, have been evaluated. Cilician coastal waters were always poor in reactive phosphate (0.02-0.05 mu M) throughout the year. However, there is a distinct decrease and seasonal changes in total phosphorus (TP) levels from the polluted inner bay (0.15-0.20 mu M) to the Cilician open waters (0.05-0.07 mu M). The surface TRIX index values, computed from % dissolved oxygen saturation, dissolved inorganic nitrogen, TP and chlorophyll-a concentrations, increase from <2 (oligotrophic property) in the Cilicial open water to levels of 3-6 in the pollutted coastal zone. In the shallow zone between Mersin Harbour and Seyhan delta, where large amounts of nutrients are discharged and TRIX values consistently >4 (showing tendency from mesotrophic to eutrophic propery), biomass level is high and the Secchi Disc depth varies between 1.5-3 meters.