The concentrations of heavy metals and organic carbon in sediment of the Homa Lagoon which is one of the most productive lagoons and commercial important active fish trap in the Eastern Aegean Sea, were investigated in order to describe the temporal and spatial distributions of metals. These results were used to evaluate possible ecological risks that could be a problem for the environment of the lagoon in the future. Sediments were enriched with Cr, Ni and considered as heavily polluted per the SQG. The C-f of Ni and Cr were presented moderate level of contamination in this area. The C-d levels indicated moderate degree of contamination at station B, C, D and E due to agricultural drainage water, industrial and domestic wastewater, are transported by the Gediz River. Sediments from Noma Lagoon were most toxic for Ni due to exceedances of the TEL and PEL values. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.