A total of 57 surficial sediment samples collected in the Golden Horn Estuary and İzmit Bay (northeastern Marmara Sea) was analyzed for the heavy metals Fe, Mn, Cr, Ni, Co, Zn, Pb, and Cu and the results were compared with various natural and anthropogenic sources. It was observed that the concentrations of Zn, Cu, Pb, and, to some extent Cr, in the Golden Horn sediments are comparable with those in most other seas in the vicinity of highly industrialized and densely populated regions. Based on calculations from the metal: Al and metal: Fe ratios, the bottom sediments of Golden Horn were found to be enriched in Zn, Cu, Pb, and to a lesser extent Cr, by factors of up to 192 compared with the regional background levels of these metals. Fe, Mn, Co, and to some extent Ni, are mostly at natural levels. In contrast, the metal levels of the bottom sediments in İzmit Bay are significantly lower and they appear to be controlled by lithogenic rather than the anthropogenic influences. Highly significant correlation coefficients between the metals Zn, Cu, and Pb are widely attributed to the common sources of these metals, the metal smelters and shipyards in the vicinity of the areas studied. Based on the numerical value of the geoaccumulation index of heavy metals, it was found that the bottom sediments of İzmit Bay can be regarded as basically uncontaminated. Exceptionally high I geo values are found for the bottom sediments of the Golden Horn, indicating moderate to extreme contamination in this region by the metals Pb, Zn, Cu, and Cr. The presence of a large number of anthropogenic metal point sources, higher river run-off via the two major creeks, particularly coastal topography and hydrodynamic conditions, associated with the very high sedimentation rates, all strongly favour the accumulation of anomalously high metal concentrations in the Golden Horn Estuary, while the opposite is true for İzmit Bay.