Forty sediment samples and fifteen water samples were collected from the Gulf of Thermaikos and the Bay of Thessaloniki in order to determine the concentration of Zn, Cu, Pb and Cr and measure various seawater parameters. The level of pollution attributed to heavy metals was evaluated using several pollution indicators in order to determine anthropogenically derived sediment contamination. Enrichment Factors, Contamination Factors, Modified Contamination Degree, and Geoaccumulation Indexes for the sediments were used to assess and visualize using GIS. Association with adverse effects to aquatic organisms was determined, using the classification of the sediments according to the Sediment Quality Guidelines (SQGs). The highest metal levels were concentrated along the shoreline of the Bay of Thessaloniki, reflecting long-term exposure to anthropogenic activities. Enrichment Factors reveal the anthropogenic sources for chromium and lead. This is supported by separate Contamination Factors, the mean Contamination Degree, and the Geoaccumulation Index. The majority of the sediment samples can be occasionally and frequently associated to toxic biological effects, according to the effect-range classification for Zn, Cu and Pb. Based on the analysis of the overlying seawater columns it appears that under the present physicochemical conditions, dissolution of the accumulated metals from the sediments is unlikely. Although the total metal content in the sediments has decreased with time, the long-term effect of the industrial and urban activities in the area is still reflected in sediments from the gulf.