The aim of this research is to determine the effects of Izmir Big Channel Waste Water Treatment Project on the sediment quality of Izmir Bay. Wastewater treatment improves the water quality. However, sediment does not respond to this treatment as fast as water column. Monitoring of bottom water and sediment quality is necessary for identification of the recovery of the whole ecosystem. For this purpose, bottom water and sediment samples were collected from three stations which are located in the middle and inner parts of the Izmir Bay on a monthly basis between January 2003 and December 2003. Values measured at stations ranged between; 0.54-12.82 mu g/L for chlorophyll-a, 0.09-9.32 mu g/L for phaeopigment, 0.05-1.91 mg/L for particulate organic carbon in bottom waters, 11.88-100.29 mu g/g for chlorophyll degradation products and 1.12-5.39% for organic carbon in sediment samples. In conclusion, it was found that grazing activity explained carbon variations in sediment at station 2, but at station 1 and station 3 carbon variations in sediment were not related to autochthonous biological processes.