Sediment cores recovered from the benthic zones of Western and Eastern parts of the Zanzibar Channel were analyzed to assess the potential ecological risk associated with heavy metals (HM), i.e., Cu, Co, Pb, Zn, Cr, Fe, Mn and Cd. Graphite Furnace Atomic Absorption Spectrometer (GF-AAS) was used to determine HM concentrations in aqua-regia-digested sediment sub-samples. The degree of contamination (Cd) of the sediment was assessed by calculating enrichment factors (EFs), contamination factors (Cf) and modified degree of contamination (mCd) relative to local preindustrial HM values. The HM enrichment in the Zanzibar Channel suggested an increase in human induced pollution resulting from dumping of untreated industrial and domestic effluents. The slight elevation in EF, Cd, Cf and mCd suggest an anthropogenic input to these coastal areas due to industrial and population increase in areas adjacent to the channel. Though the potential ecological risk (PER) and its index (PERI) are elevated but their ecological risks were still very low. Thus the need for mitigation and monitoring processes is vital to avoid further pollution in the channel and its surrounding ecosystems.