In this study, a simple site-specific index entitled "Discharge Effect Index (DEI)" was developed to rank and control the potential risks of point sources discharges effects to Ergene River and its branches. The basin is densely populated and heavily industrialized and all the water bodies in the basin are effluent-dependent or dominated. A case study is presented to assess the most important pollution parameters in the water bodies and to evaluate relationship between toxicity to Vibrio fischeri organism and chemical parameters in receiving waters. The aim of the study was to develop a simple site-specific control approach for seriously polluted and effluent-dominated water bodies in this developing country, Turkey and guide to decision makers about controlling point sources pollution in such heavily industrialized basins and achieve 'good chemical status' in ambient waters. The results of the study should be useful to encourage site-specific policies on point sources pollution especially to who had such these pollution problems in their receiving water bodies.