Port Pirie is the site of the largest lead smelter in the world, depositing 250 t of zinc, and 100 t of lead annually into Spencer Gulf. Barker Inlet is adjacent to metropolitan Adelaide, and receives unknown quantities of urban and industrial discharges. Both areas are sites of major commercial and recreational fisheries, contained within delicately balanced marine wetland ecosystems, comprising large areas of mangrove and seagrass habitats. Aldrichetta forsteri and Sillago schomburgkii are major species within these fisheries and as estuarine-dependent species were chosen for this study as indicator species for the detection and monitoring of pollutant impacts in the nearshore marine ecosystems of South Australia. Seston sediment collectors were deployed at each site and analysed seasonally for the presence of cadmium, lead and copper. Flesh samples from A. forsteri and S. schomburgkii were examined seasonally for the presence of cadmium, lead and copper and the results correlated with levels found in the seston sediment at each site. Metal concentrations were also correlated with a biomarker of genotoxicity measured in the same animals (micronuclei in erythrocytes) that were reported previously. Seston levels of cadmium, lead and copper were highest at Port Pirie, followed by Barker Inlet and were lowest at Wills Creek, with cadmium undetectable at the latter site. Metals in seston varied considerably with season, with generally higher levels in winter samples. In fish flesh, metal levels followed broadly similar trends as for seston. Spearman rank correlations between metals in seston and in flesh were strongly positive. There was also a significant correlation between flesh concentrations of each metal and the frequency of micronuclei in erythrocytes. This study has shown that seston concentration of pollutant metals are high in areas of industrial activity, and that these levels are also reflected in metal content of fish flesh. Mean flesh levels of cadmium and copper did not exceed Australian health based maximum permitted levels of fish for human consumption, whereas flesh levels of lead in fish from Port Pirie and Barker Inlet exceeded these standards in each of the seasons monitored. This may represent a significant dietary source of lead in humans, especially at Port Pirie where human lead exposure from terrestrial sources is important. There may also be the potential for accumulation of metals in residents of metropolitan Adelaide whose diets are high in fish (and/or crustaceans), particularly estuarine-dependent species, such as A. forsteri and S. schomburgkii. The study also showed that a non-specific biomarker of genotoxicity (micronuclei in erythrocytes) is potentially useful as a monitoring technique in fish species to evaluate their exposure and genotoxic responses to pollutants in South Australian waters. These data represent a snapshot of the current situation in this area and may act as background levels against which future improvements or decrements in water quality may be compared.