More than 65% of the South African coastline is threatened as a result of pollution, a large proportion of which is land derived. To date the majority of published data on metal monitoring has been on limited regions or once-off sampling events. In this paper, we present the first data on metal exposure at sites along the eastern seaboard of South Africa in resident brown mussels (Perna perna) from six harbour sites (Cape Town, Durban, East London, Mossel Bay, Port Elizabeth and Richards Bay Harbours) over a two-year period (2008 and 2009). These data do not represent historical or the current metal exposure levels, but rather an indication of the degree of metal exposure fluctuations over two years at the same site. Metal accumulation of aluminium, arsenic, cadmium, cobalt, chromium, copper, iron, manganese, molybdenum, nickel, lead, selenium, strontium, uranium and zinc was determined by thermo-inductive coupled plasma mass spectrophotometry. The results showed marked fluctuations in metal concentrations between years and identified Cape Town, Mossel Bay and Port Elizabeth Harbours as those sites where mussels had the highest metal levels. Statistically significant variations in metal concentrations were observed between the two sampling periods and the six harbours. Metal concentrations decreased from 2008 to 2009, which was largely attributed to changes in ambient metal concentrations, as a result of variable non-point discharges of metals into the harbours and larger-scale oceanographic changes in upwelling events. The results further emphasise the necessity for annual monitoring of the South African marine environment.