A focused diagnosis of ecosystem health in two South African estuaries (Kromme and Gamtoos) was conducted. Four pollution indices were used, i.e., geoaccumulation (Igeo), ecological risk (RI), contamination factor (CF) and pollution load index (PLI), to assess toxicity levels of metal contaminants in relation to background values. The Igeo results (11.1 %) can be classified as contaminated, with Cd, the only element with high values in both estuaries. Likely sources (herbicides, pesticides) of Cd are used in the agricultural dominated catchments. There was a high concentration of Mn (13.4 ± 2.51 and 12.3 ± 1.13 μg·g−1) and Fe (1289 ± 243 and 1291 ± 130 μg·g−1) at site 4 for Gamtoos and Kromme estuary respectively compared to the other metal elements. Although results indicate low metal contamination, with increasing global anthropogenic pressure, continuous monitoring should be prioritised to assist in managing estuarine systems that support a wide range of socio-economic and ecosystem services.