The bay of Souda is an important natural harbour in the north west of the island of Crete. Its area is about 21 Km(2) and its maximum depth 210m. The bay receives the inputs of the Moronis River that discharges at the inner part of the bay. The commercial and the naval port, as well as the city of Souda are located at the west-south coast of the bay. The aim of this work is to assess the levels and the spatial distribution of several heavy metals and organic carbon of the surface sediments of the bay and identify the major sources of pollution. A sampling cruise was carried out during February 2008 in a sampling network consisting of one estuarine, two coastal and ten marine stations within the bay of Souda. The sediment samples were collected using appropriate sediment samplers. The contents of the sediments in nine metals (Zn, Mn, Pb, Ni, Cd, Cu, Fe, Al and Hg) were determined by Atomic Absorption Spectrometry after total dissolution of the sediment samples by strong acids. Total Organic Carbon (TOC) was determined by a standard volumetric method. According to our results, elevated values for the majority of the studied metals were determined in the central and western part of the bay near the cove (mean values for Zn, Pb, Cu and Hg were 95.5, 42.4, 39.2 and 0.128 mg/Kg, respectively against 36.2, 22.2, 17.1 and 0.053 mg/Kg respectively at the rest of the bay) indicating that the discharges of the river Moronis, the activities of the Naval Base as well as of the Commercial Port, influence the bay's sediment as well as seawater (Dassenakis et al, 2012). In the case of Cadmium an opposite trend was observed, as the highest values were detected in the south part of the bay's entrance (0.144, 0.109 and 0.06 mu g/g for the estuaries of the river, the entrance of the bay and the rest of the bay's area respectively). This trend is not clear for Nickel and Manganese. A statistically important correlation (according to the t-test) between Al and Fe as well as between Al and Mn (r = 0,989 and 0,809 respectively) was found, indicating a common origin, probably geological, for those three metals. According to the SQGs, none of the metals studied exceeded the perspective ERMs/PELs, the values above which adverse effects on benthic biota are frequently observed. However, the levels of Cu, Pb, Zn and Hg found in the sediments of the river estuary and close to the naval base exceed the low-range values (ERLs/TELs). Therefore, pollution control measures and monitoring programs including toxicity tests on biota are needed for protecting and/or restoring the sediment quality. The values of TOC measured were lower than 0.3 % (w/w) indicating a relatively low content of the sediment in organic carbon. In conclusion, we can say that the surface sediments of the bay are not enriched in metals and TOC, with the exception of the areas near the river's estuaries and near the naval and commercial harbour. Nevertheless, the values measured are lower than the ones prevailing in other Greek marine areas near big cities such as Saronikos gulf, Thermaikos gulf and South Evoikos gulf.