The distribution of heavy metals (zinc, cadmium, copper, iron, manganese and lead) was investigated in seawater and in sediment samples from the East London and Port Elizabeth harbours. Both are ports of major importance to the area. The aim was to assess the impact of potential pollution sources, mainly from the cities' formal disposal to the sea, from industry and from dockyard and shipping activities around the harbour. At the East London harbour, metal concentrations in sea water range from 0.2 to 72.0 mg·l -1 for Cd, from 0.6 to 42.6 mg·l -1 for Cu, from 2.4 to 183.0 mg·l -1 for Fe, from 0.6 to 16.3 mg·l -1 for Pb, from 0.9 to 23.9 mg·l -1 for Mn and from 0.5 to 27.6 mg·l -1 for Zn. In sediments, metal concentrations using the total digestion method range from 0.12 to 1. (dry weight) for Fe, from 9.0 to 61.9 mg·g -1 (dry weight) for Pb, from 103.0 to 499.0 mg·g -1 (dry weight) for Mn and from 18.8 to 126 mg·g -1 (dry weight) for Zn. The results are indicative of the contribution of heavy metal pollution from storm water drains and streams which carry runoff from industrial, urban and residential sources. Ship repair activities are also suspected to be responsible for elevated concentrations in the upper reaches of the harbour.